destroyed contents of directories.

[godel fishbreath]

Ok, recently I had a directory wiped clean.
I was using this app to transfer files to a new clean place.
I expected that the files listed in the compare would show up in the new drive. I did not pay much attention. The whole got wiped clean, no warning.
How to ensure that this does not happen again?

[Plerry]

After running a Compare, carefully inspect if the proposed actions meet your expectations and intentions.
If so, only then execute the actual sync.
And afterwards inspect the sync-log to see if any of the planned sync actions may have failed.
Only after having built up confidence that everything works as intended, you should step to running automating sync tasks.

[VladimirII]

Long ago we had a machine with not enough drive space. Probably months later we found out some folders are empty. Arguing the lack of space caused it. So the moment the space lacking machine synced back deleted it. (Although the folder names itself existed)

Have you checked the recycler? Is all moved there?

Yeah two way synchs need special attention.