isync has become a bit more strict about semantically questionable configurations; maybe you ran into that.
or maybe you ran into the bug fixed by 8c781d4f. i need to finally release 1.5.1 ... please post the Store's config, and the actual file system layout (find <Path> -type d; excerpt sufficient). also run `mbsync -ls <store>` to get an idea what isync thinks is actually there.