I ran into an issue where files I deleted from Boxcryptor on macOS did not propagate to OneDrive. (Deleted files remained on OneDrive.) Added files did sync. I only noticed it when I was viewing Boxcryptor on my iPad and saw files I had deleted.
I was able to fix it by logging out of Boxcryptor and then back in.
I do not know how long it was not working. There were never any error messages. It was frustrating, but I suppose it's better than new files and changes not being synced.