I think my stuff in the cabinets from before the update disappeared since I can't find my spoiled strawberry seeds anymore. They were in my cabinet. Anyone know what this is all about?
Some items got moved around during the R3 release, also, if they were not in a bag prior to the new release, perhaps they are in a moving box or on your floor somewhere? Maybe you moved them into a new place whilst cleaning up your moving boxes?
If they are truly missing, file a bug report. The staff can track what you had and help :)