A similar test might be to uninstall your current 2.0.6.100 and downgrade to the previous Canary 2.0.5.114_canary_2021-03-10, Alternatively, do you recall if 2.0.6.100 is when messages began?
A somewhat less disruptive real test would be to unzip 2.0.5.114 and add a file to Duplicati area:
/usr/lib/duplicati/BouncyCastle.Crypto.dll
Theory behind this is that MailKit.dll 2.3.1.0 has a dependency on MimeKit >= 2.3.1 which has a
dependency on BouncyCastle >= 1.8.5 which Duplicati shipped until 2.0.6.100 removed its use,
possibly not realizing that there was an indirect use through MailKit which is used to send email.
Weighing against the theory is that 2.0.6.100 has been out four months, so who gets this or not?
Regarding NFS, no ideas yet, but did anything known change around then that might be related?
Nor does it support SMB. Storage Type is Local folder or drive I guess. OS does the rest.
Do you mean the allegedly missing files are there, or just something is there that looks a backup?
An Information-level log is good to get. It shows the remote file actions and the missing file names.
Use About → Show log → Live → Information or log-file=<path> and log-file-log-level=information.