https://streamable.com/0xs7vr

Apotheosis makes some heavy changes to the Vanilla Anvil which is likely the root cause here. Still, this only happens in Better End Anvils, so it may require some sanity checks on your end to deal with it.

Reproduced in a test instance with only the following:
Forge: 36.0.40

Apotheosis-1.16.3-4.4.1.jar
betterendforge-1.16.4-1.5.0.jar
jei-1.16.4-7.6.1.71.jar
Placebo-1.16.4-4.4.1.jar
trashcans-1.0.8-mc1.16.4.jar

Steps to reproduce:

1. Place a tool in a Better End anvil.
2. Place an Enchanted book to combine with the tool
3. Complete the craft and exit the anvil. All the items used in the craft are returned to you.

This also happens when combining tools or even just renaming things.

Very weird issue, i will take a look at what Apotheosis does with anvils, thanks for reporting this!

So, they basically add a tile entity to the anvil block..and then they do some check that involves this tile entity when the player takes the output item from the anvil(which obviously fails with BetterEnd anvils). I think i fixed it just by conditionally adding their tile entity to our anvils...so it should be working now, let me know if you find any other incompatibility with apotheosis

Awesome, will check it out as soon as possible.

I quickly realized that, even if this bug has been fixed, Apotheosis anvil compatibilty is far from being complete, as the behaviour of their anvil, aswell as their enchantability has to be replicated on my part if we want BetterEnd anvils to fully work as Apotheosis wants