Items are wiped from the players slots when the stack is auto-restocked by Quark's feature.
This bug occurs intermittently, and has been experienced by 2 people I play with on a private server. I have currently not been able to reproduce it myself, so am unable to give a good insight as to what might be happening exactly. I suspect the lines of code linked below may be causing an issue if the client and server have a slight de-sync though.

Mod version: r1.2-95
Forge version: 1.12-14.21.0.2331

Relevant line of code: AutomaticToolRestock.java#L111-L112