Irreversible elements that are relatively unimportant
Variation in status
Characters above level 2 will probably have different stats when you recruit them. For example, the stats of level 99 Sheena and Kuromimi will change every time you reset and recruit them again.
The stats that increase when you level up will also vary depending on the person playing the game. However, when I tried the trick to raise the main character from level 36 to 96 several times with the same save data, it always ended up at the same level of 96. Therefore, if the stats at level 96 are lower than usual, I don't think there's any point in immediately going from level 36 to 96 again (it's unclear at this point what conditions cause the stats to change).
I think that stats will eventually settle at roughly the same values (at level 99 there might be a difference of 10 or 20, but I don't think there will be a difference of 100 or 200), so unless you're particularly picky, I don't think there's any need to worry about it.
In addition, the stats other than "Strength" and "Technique" - "Defense, Speed, Magic, Luck" - can be increased to their limit by using items called "Crest Fragments" that can be dropped by monsters or obtained in mini-games (although this takes a lot of time... In the PS version, there is a way to increase stats to their limit with crest fragments, so I think it is possible to increase stats relatively quickly. If you use this trick, you can also increase Strength and Skill to their limit with crest fragments).
Also, if you attach the Earth Crest Fragment, which can be obtained by monster drops, to a weapon, the Skill value will increase by 2, so regardless of the device, Skill can also be increased with items.
In other words, if you take the time, you can increase all stats except for "Strength" to their limit with items (in the PS version, you can use a cheat to increase Strength and Skill to their limit with crest pieces). The limit for a stat is 255, and you will no longer be able to use stones on that character. Therefore, a stat will not go beyond 255 and go back to 1 (confirmed in both the PS and PSP versions).
Rare items
Here are some rare items that will never come back or be reacquired if sold, thrown away, used, or given to or housed by characters who leave during the game (Ted, Odessa, and possibly Pern and Gremio...). However, with the exception of the Blinking Hand Mirror, there is no particular problem with having or not having these items in the game.
Item handling when companion characters are lost
Ted and Odessa's belongings will disappear.
Gremio will lose the crest he possesses, but his belongings will automatically be moved to the warehouse. The crest will also return if Gremio revives (because Gremio possesses it).
Parn will rejoin the party with the items he had at the time of the first separation at the beginning of the game. Therefore, Parn can be used as a warehouse for items that were obtained early in the game but are not used right away (such as treasures and crest fragments). When Parn is defeated by Theo, Parn's belongings will automatically be moved to the warehouse.
Even if Gremio or Parn dies when there is no warehouse in the base yet, if a warehouse is created in the base, Gremio or Parn's belongings will be in the warehouse.
I haven't researched what happens to the possessions of characters who die in battle, so I don't know.
About the crest pieces
Of the crest pieces, Strength (1), Skill (2), Fire (1), Lightning (3), and Wind (1) are valuable because they are not dropped by monsters and the number that can be obtained is limited. However, since the Strength and Skill crest pieces only have the effect of increasing the status by +1, it is not particularly difficult to have them in the PSP version. In the PS version, you can use the status increase trick to the limit, so it is important if you want to use it.
List of rare items
Celadon Vase
Dropped by the bushy creatures around the early Gregminster. This is an item to display in the bathtub. You can see its appearance in "Old Book 7". When you are able to go to Gregminster again at the end of the game, the bushy creatures will no longer appear and you will no longer be able to obtain it.
Octopus Pot (Treasure Chest in Mt. Koro)
You can get one from the treasure chest, and it is dropped by the bushy creatures around the early Gregminster. It is an item to decorate the bathtub. You can see its appearance in "Old Book 7". When you can go to Gregminster again at the end of the game, it will be impossible to get more than one because the bushy creatures will no longer appear.
Lightning Crest Fragment (Treasure Chest in Mt. Seifu)
Wind Crest Fragment (Treasure Chest in Mt. Koro
Seal Ball of Separation (Treasure Chest in Mt. Koro)
Deals double damage to enemies than a normal attack, and the user of this emblem becomes unbalanced for one turn. I think this emblem is suitable for Victor, whose normal attacks are hard to hit, but it's not a problem if you don't have it. I often equip Victor with the Divine Movement emblem to move the main character faster.
Crest of Power Fragment (White Treasure Chest at Lake Trang)
Fire Crest Fragment (Treasure Chest in Lepanto Mansion)
Slip-Through Tag (Initial possession of Klin and Stallion)
Unlike normal slip-through tags that can be bought at the tool shop, these do not disappear when used. They sell for 0 and cannot be sold. If you deposit them in the warehouse (including depositing them by "peeling them off"), they will return to normal slip-through tags. Since Sauniere Prison is a prison, it is only natural that in the latter half of the game, enemies have measures in place to prevent slip-throughs, making it impossible to use slip-through tags. For example, slip-through tags cannot be used in Necrode Castle, Moravia Castle, Sasharazad, and Gregminster Castle.
Gale Sealing Ball (Pannu Yakuta Castle Treasure Chest)
2x Speed.
Lightning Crest Fragment (Treasure Chest in Pannu Yakta Castle)
Blinking Hand Mirror (Teien's Inn)
You can throw them away, but it's best not to.
Sealing Ball of Fire (Treasure Chest in Scarleticia Castle)
After the attack of the character who possesses it, all inactive characters will act before the opponent, ignoring their speed value. If you equip a fast character before a boss battle, even a character with a low speed value can use recovery magic before the enemy's attack.
Ruler, salt, soy sauce, soap
This is an item required to recruit Sayla in Kirov. If you trade multiple times before recruiting Sayla, you can keep it. If you deposit it in the warehouse, you can trade again, so you can get more than two. You will always have one soap in your possession even if you do nothing. However, there is no use for it. It is just an item to keep in the warehouse.
Skill Crest Fragment (Treasure Chest in Cave of Kron Temple)
Seal Ball of Return
Eikei resides within. When there are two or more enemies, it can perform two direct attacks (sometimes it doesn't).
Crest fragments to attach to weapons
There is a limit to the number of attribute-imparting emblem fragments that can be attached to weapons other than "Water Crest Fragments" and "Earth Crest Fragments." Also, if you attach a crest fragment with a different attribute to a weapon with a crest fragment attached, the original crest fragment will disappear (meaning you cannot reuse them like equipment).
For example, if you attach a crest fragment of a different attribute to a weapon with a "fire crest fragment," you will never be able to prepare another weapon with a "fire crest fragment" attached to it (because you can only obtain one "fire crest fragment" per game).
Also, the crest fragments attached to a weapon cannot be removed. Therefore, once a crest fragment has been attached to a weapon, it cannot be returned to a normal weapon with no crest fragments. However, it is possible to change a weapon to a different attribute by attaching a new crest fragment with a different attribute.
For the past 30 years, I think that "attribute crest fragments" and "attack together" have been mysterious areas that no one has tried to touch on in any Japanese Suikoden I strategy site, or that the information they have listed is incorrect (for example, it has long been said that Lepanto + Irene's attack together is a fire-attribute attack, but in reality it has no attributes. However, strangely enough, almost every site insists that this attack together is a fire-attribute attack).
Early Gregminster-related
In the beginning of the game, you can get "100 pots" by examining the right one of the two armors in the room opposite Clay's room on the first floor of Gregminster Castle. When you are able to go to Gregminster again at the end of the game, you will no longer have the 100 pots. However, since it's just a matter of whether you can get the 100 pots, I don't think it will be a big problem if you don't get them.
Also, you can only enter Gregminster's house, Miluihi's house, and inn in the early game (you can enter Sonia's house even at the end of the game). However, there are no items in those buildings in Gregminster, and no monsters appear, so you shouldn't have any trouble.
The only shop where you can buy wing boots is the armor shop in early Gregminster, except for your headquarters. Items sold at the tool shops and armor shops in each town cannot be purchased from your headquarters unless you talk to the tool shop and armor shop in that town once, and since the items sold at the tool shop and armor shop in Gregminster are different in the early and later stages, if you have not talked to the armor shop in early Gregminster, you may not be able to buy wing boots from the shop in your headquarters (unconfirmed). However, wing boots can be obtained even if you cannot buy them at a store because they are dropped by ninjas (Moravian Castle).
Monsters that appear around Gregminster are different in the early and later stages. The Bushy, which drops the Pot of Sacred Blood and the Octopus Pot, only appears in the early stages. The Boar, which drops the Earth Crest Fragment, will also no longer appear, but the Black Boar in Mount Seifu also drops Earth Crest Fragments, so you can get them there.
Magician's Island, Lake Tolan's White, etc.
Magician's Island, Lake Tolan's White, Elf Village, Hidden Crest Village
The islands, castles, and villages you will visit in the first half of the story, and the villages you will visit in the second half, can only be entered into the caves of these islands and castles at that time, and you will never be able to enter the caves of these islands or castles again after that. You will no longer be able to enter the Elf village once you have given the Running Water Stick obtained from the Dwarf Kinko to the Dwarf village chief. You can also only enter the Hidden Crest Village once during the event where you enter it, and you will never be able to enter it again after that.
However, it won't be a problem if you can't enter. The only valuable item is the treasure chest "Power Crest Fragment" in the cave in Lake Toran White, and other items can be obtained later by other methods. The slugs that appear in Lake Toran White will drop the Guardian Crest Fragment, but since slugs can also drop medicine, it is relatively difficult to collect the Guardian Crest Fragment with slugs. If you want the Guardian Crest Fragment, I think it's better to get it from the snails in Koro Mountain early in the game.
Also, only the Elf Village armor shop sells collars and feather ornaments, so if you want to perfect the items sold at your home base armor shop, be sure to talk to the Elf Village armor shop. Your home base's tool shop and armor shop will not start selling items sold in the town unless you talk to the town's tool shop and armor shop at least once.
Other
The zombies in Necrod's castle who give you hints on how to beat the game will disappear after you defeat Necrod.
Blacksmith Attack
The blacksmith attack is a joint attack that can be performed by any four of the five blacksmiths Marth, Meese, Moose, Mace, and Morse. At the end of the game, after the final Gregminster battle event, Flick and Victor are forced to join the party, and you will no longer be able to include the four blacksmiths in your party, so you will no longer be able to use this joint attack.