I’m glad you got it going. I don’t know what’s up with missing files. In theory, anything Duplicati does to the local filesystem should eventually get synced to the remote, but one loses the better tracking done by Duplicati. One can even get files uploaded in unknown order chosen by the sync software. This can leave who-knows-what on the remote to restore from if the local drive breaks before finishing the sync.
Knowing you were pointing to a local folder means this is possibly a seeming bug in mono described at
Backend quota has been exceeded after apparently successful backup
Warning Backend quota is close to being exceeded
Possibly your quota information came from a local filesystem (I can’t explain in detail). Maybe try df -k?
Secure Socket Layer (SSL) / Transport Layer Security (TLS) is good for troubleshooting certificate fails.
If you’re missing ca-certificates, and don’t want to get it separately, I think mono-complete includes that.