Forwarded from MinecraftModDevelopment/MMD-Dev-Server#147 by @MrTaco9001 :

Right clicking on a colassal chest makes all the items in my inventory go away. They don't get deleted but they only way to get them back is updating my inventory.

This has been fixed in 9132afa, and is included in the new release.
I'll post an issue to request an update.