I had that problem a few versions before
Now i'm so scared it will happen that i only make changes in 1 system at the time
then i aply changes and save the mod
then i quit FLE and restart it for the next changes to be sure it won't mess things up (i found out that fixed the problem for that version that didn't find the emptyresource.dll file)
sounds like some extra precoutions , but at the end it pays out since losing your data is a lot more work its just a idea if u continue having that problem even with the latest version