You losing your item due to desync is sad, yes, but life goes on.
Item loss also happened on the SEGA servers and it's mostly due to the fact that PSOBB is not entirely server sided so the server and client can go out of sync.
Causes for item loss would be a desync and selling an item or dropping an item when inventory item IDs aren't in sync.
I'm working on two things that will help mitigate this issue but if you're constantly desyncing while playing the game, you should try to either improve your internet connection (bad wireless can cause desyncs) or try playing on another ship.