Linux seaf-cli not downloading files

I seem to have a weird problem.
seaf-cli is running on my smb server (DYI NAS) where it then syncs everything to my seafile server, at some point my seaf-cli had some issues syncing files and I didn’t notice, nut sure why but that isn’t really the issue.
it happened before, I just started the seaf-cli and everything was back to normal, unfortunately not this time.
at first I had some issues about not being able to merge, I ran the seafile fsck on the server, all is fine. Then I desynced on the the linux SMB Server running seaf-cli and started the sync again, no more merge errors but files are missing.
I was expecting to find some files but couldn’t, looking on the seafile server I can see the files but they are not being downloaded.
if I create a dummy file or directory on the smb server, it gets synced to the seafile server. If I delete this dummy file from the seafile server (through the web interface) then this file will also be deleted on the smb server.
unfortunately the files that I see on the seafile server are not being synced to the client.

What’s the correct procedure here?
how do I get them both back in sync? download to new directory and rsync? Assume everything was uploaded, delete the directory and start seaf-cli download again?