The bug was identified. And Realmac confirmed they could reproduce it. You should contact Realmac support to ask when they might fix this in RapidWeaver 7.
Unfortunately the bug is related to saving duplicates of your project file. So in a horrible irony the fact that you keep losing data is encouraging you to do the very thing that is likely triggering the bug and… making you lose more data. 
The workaround that I suggested for others is very simple and seems to be very effective:
-
Always make duplicates of your file in the Finder when RapidWeaver is not running at all.
-
Never use the Save As… command in the edit menu or Command-Shift-S.
I believe this will entirely avoid the problem. If you still notice a problem with similar symptoms even though you never use Save As… then it’s likely to be a different problem and we should start a completely separate investigation.
Isaiah
// @dan