An update. I originally thiought I only had about 200 files but over the course of the last few months more and more keep showing up. Enough that I no longer use DTTG at all for fear of corrupting stuff and am moving things out of DT on the Mac as fast as I can. In the more recent problems I have at least been able to go back to my backups and find the files and recover them but the bug is still there.
I’m using WebDAV to sync and am running the latest versions of DT and DTTG.