Science packs can be regenerated, and dont remember their wear if ya take the worn pack out and swipe it back in. take near dead pack out swipe it back in new science pack..... might work for re-pair packs now that i think about it.

Yup any tool is repaired when swiped into a chest.

0.16 changed decaying items to clump into one stack instead of being broken up. Check to make sure your stack size isn't lower when picking them up.

I already know about this, but it is too hard to fix for being a relatively minor issue. The modding API only has very limited ways to handle damaged items and most functions I use in the mod just ignore durability, so I would basically have to rewrite everything...