alright. I have a tentative list of items (see attached txt file) that (1) are not useless and (2) shouldn't disappear if taken on quests. Seeing as I only have acess to 12 boxes in-game right now, I'm uber not sure about anything after the Prime Redhelm Scraps (especially the last few items which I presume are DLC items). I still need to double check most things in boxes 1-12 for any account/supply items I may have missed as my documentation was a little lacking (and I was focused on getting the pack-rat guide before actually putting these in my game).
A couple of notes:
I removed the following items numbers (in decimal, not hex) due to being unsure what they were/them having unknown item markings. I'll test them later to make sure they're useless before completely writing them off:
92,131-205,1364-1367,1556-1658,1661-1663,1889,1890,1907,1908
everything past item #1932 (Arthur's Armor) showed unknown item, so I'm assuming they're all not valid items or are dummied out
I also removed a few lower tier items (like Demondrug) while leaving the stronger variants (like Mega Demondrug). Aside form these and the account/supply items, all items needed for crafting/combining should still be there.
As I stated above: Charms and shards disappear on quest start like account items/supply items/0 quantity inventory entries, so they are not included.
I'll update with a final version of the list when I finish testing everything, which should be tomorrow night (as pertains to EST)