No, I just use the one account.
I do have both SeaDrive and the normal SeaFile Client (7.0.7) on the same machine. I mainly use files in directories synced by SeaFile but use SeaDrive for accessing less frequently used files (and also when I need to search by filename as I’m using the Community Edition of the server which doesn’t allow searching).
I’d been cleaning out files from one library (in a SeaFile synced folder), but otherwise I hadn’t done anything unusual. So I can’t really throw much light on the precise circumstances which triggered the issue (nor reproduce it).
However, the results sound very similar - in my case the files were deleted in about 10 of 30 libraries, the remaining ones being unaffected, and in the 10 libraries which were impacted almost all files were deleted (there were a couple of cases where a few files in the root of the library remained), but all directories remained.