The item doesn't reappear in inventory until the character that uses it gets their ATB refilled.
i don't think you need to have their ATB refilled, but rather change from one character to another with X or Y. iirc, the Item List you see can't update while you're just sitting on a character's main battle menu as somebody else is altering the Item inventory. so it's the same deal with Stolen items. X/Y triggers the "refresh".
or besides X/Y, having a character take a turn, so another gets first in line. iow, i think it's tied to having the triangle cursor switch onto a new character.
anyway, it turns out that the inventory adding, after the C2/54DC call in C2/62C7, has two steps:
1) Copy $2E72-$2E76 buffer to a $602D-$6031 [plus offset] buffer , as many as 4 times
2) Copy $602D-$6031 buffer entry/ies to Item menu
C2/62C7 does the first step. if we're at the end of battle, C2/492E does the call to handle #2 (one call, which loops if there're multiple buffer entries) right after that. if we're mid-battle, we're reliant on the triangle cursor switch. or if that never happens, then it's addressed when the battle is finished.
this explains the lag in the Item menu update after acquiring an item, if we didn't move the cursor off of a given character in the process. this can be prolonged awhile, if we have characters acting automatically. i don't think there are any problems beyond wait (i.e. no item loss), since the $602D buffer apparently has 16 entries maximum, which is plenty. (6 stealings + 6 Metamorphings = 12. though Pandora's Box can exceed that if you indeed implemented the multiple stolen items per enemy?) the only way i can think of to exceed this in a normal, For-What-Ails-Ya-fixed game involves a character Life 3'ing themselves, trying to use an item, and coincidentally getting killed before they can act -- and doing this at least 5 times (12 + 5 > 16).
EDIT: ok, that last sentence is wrong, because having their main menu come up again when their ATB refills after revival will refresh the Item menu.
elsewhere (i.e. won items), Square just calls C2/6279, which handles Steps #1 and 2 in one shot. so why do they split up the steps in these cases? my guess is speed. at battle end, C2/492E doing step #2 for all characters with one Bank C1 call (LDA #$0A / JSR $6411) is faster than having C2/62C7 do this far call for each character separately.
however, as mentioned, Step #2 doesn't always instantly follow #1 mid-battle. since i don't favor editing C2/62C7, a fix for the lag would be to have C2/1423 do a "LDA #$0A / JSR $6411" right afterwards. a far call consumes some cycles, but it can't be *that* bad.
to refresh: this lag behavior is in the original game, and isn't caused by the "For What Ails Ya" patch.