You are correct and I know the development team that works on sync has some fixes in the works which should be coming out in the next few weeks. I'm sorry for the difficulties you've encountered. Hopefully this issue will be remedied permanently soon.
my office is still having this issue. today is even worse because CC put all files in the trash but not the folders so now we don't know the projects each file came from. it's gonna be a long day figuring it out.
this service is shit tier. selective folder sync would have minimize a lot of the issues we are having too.