RFTools crafter eats stacks of items as per this github bug report Crafter eats my stuff · Issue #276 · McJty/RFTools · GitHub It ate a while stack of advanced induction cells from me which seriously annoyed me and has since eaten half a dozen other hard to make items. According to the mod creator the subsequent update should fix this issue, since the latest version is 3.50 doing a pack update would surely help.
We can't update until there is another modpack update which fixes the multiplayer issues but I think the modpack author doesn't care about that.