I've been having the same corruption problems w/ jemplode 69.000001 as well. Problems started around versions 66-67. I'm no expert on the workings of this app. However, if I force myself to close and re-load jemplode b/w every sync, database corruptions have disappeared. I even do this for small stuff, like mods to config.ini. It's a pain, but it works.

I've become addicted to the soup playlists and have developed some similar procedures for making sure that they (and my personal playlists) don't get hosed by jemplode.

Assuming only regular playlists and no soups:
1. Enable Soup updating in jemplode. Add soups and sync. Close and re-start jemplode.
2. Disable soup updating. Check all personal and soup playlists look good. Enjoy soups!

As music tracks accumulate on my PC in the future, I batch them together, add to personal playlists and erase/rebuild soups. Soup updating of existing soup playlists has trashed by database many times in the past, so enabling/disabling of soup updating and erasing/rebuilding of soup playlists has been the only way to keep jemplode from destroying the db.

On next music upload:
1. Add tracks to personal playlists, keeping soup updating disabled. Sync player. Enable soup updating. Close and re-start jemplode.
2. Erase soups and sync. Close and re-start jemplode.
3. Rebuild soups from stratch. Sync player. Disable soup updating. Close and re-start jemplode. Enjoy more soups!

How time consuming! Hopefully, the multiple sync in one session and soup updating will get fixed down the road.