There is definitely a flaw in how Mailsync stores sent mail. It results in duplication in some cases, and deletion in others.
@chmatonakis I think your situation might actually be a bit different from this bug. Would you be willing to create a new bug report about this? The template does ask for some additional info. (P.S. We need the actual Mailspring version number. “Latest” won’t help us as soon as the next version comes out.)