scientiae: IIRC the problem happens when an object is placed in another's inventory (via the right-mouse pop-up menu option when selecting a companion) — after a chapter increment, it can disappear.
PeterScott: That's a different issue and expected. IIRC, Companions "new" in each chapter.
Therefore it is a (known) limitation in the earlier games (I seem to recall there was no companion inventory slippage in
Hords of the Underdark) that in hindsight is predictable (and so avoidable) but is a quirk nonetheless, and especially if the player has migrated from one of the Black Isle games, where there is no companion reset with a new chapter.
The games are remarkably similar except for this limitation. This game was released after the others, so this might add to the confusion.
Observe that, in
Baldur's Gate by contrast, all the companions' inventories are part of the global accoutrements of the player, merely serving as local caches for their consumables (like ammunition) and of course to outfit them with their particular weapons etc. Imoen in
BG, for instance, can identify with a spell or a scroll; this is triggered when viewing any unidentified item —— through the standard inventory dialog —— providing
the same character who holds the item has the spell memorized or the scroll in their inventory. So it is a character based process, unlike
Neverwinter Nights, where the (initial) game is all about the protagonist with the companions providing banter and martial support. It is also possible to use companions as pack mules, too, but if stuff disappears and the player doesn't know why, this becomes risky when it shouldn't be.
This might be the root of the confusion for the OP. The original
NwN uses companions to help cover the lack of skills for the player character. Playing a mage I have given the half-orc beserker a (very expensive) magic sword only to find it missing a short time later and lamented the opportunity cost that might have yielded a sackful of potions instead.
