From Discord:

Heyo, my interface's autocrafting keeps randomly breaking, is my setup wrong? Manually autocrafting via a crafting grid still works. Destroying the interface / clearing the requested items etc. doesn't reset it.

The only way I found to reset it is:
Break the interface with the autocrafting upgrade is still inside
This destroys the autocrafting upgrade (it doesnt drop)
I place the interface again and put in another autocrafting upgrade

Playing ATM10 btw.
Chunks are loaded 24/7

edit: v2.0.0-beta.2