(Assuming you're asking me...) I'm not fully clear on profiles, but I don't think you can do selective sync'ing by folder. It's all or nothing; you either sync a profile with a target or you don't.
I didn't set up sync'ing for the second profile I created. I only imported .jex files, and I deleted the notes in the .jex files from my primary (sync'ed) profile.
And I also haven't seen a way to remove a profile. I don't need it now, but I could envision a future where I would, so it would be nice to know how to do that.