Don’t let anything make up names. Names matter. Extra files (as mentioned before) can cause trouble. Missing files can cause trouble. Duplicati checks for the names it expects and complains on mismatch.
Deletions should be synced. You want an exact duplicate, except timestamps don’t matter to Duplicati. Typically they matter to the sync program though unless “sync” is copy of all the files to a cleared area.
Backup directly to two locations is a post from @drwtsn32 describing actual use of the sync strategy, replacing a two-independent-backup approach, and describing dislike of running two separate backups.
The drive rotation idea I cited above where the DB is on its drive is only possible because it’s a drive, but avoids the backup-twice and backup-differences issues – but it means only one current backup at a time. Offsite drive is good for disaster recovery, but it’s slightly stale. A network offsite is easier to keep current.
Files at the backup destination aren’t changed due to source changes. Any new data goes into new files.
There might be one exception (untested) to no-changes design. A purge might overwrite a current dlist. Alternatively maybe it writes a slightly different name, e.g. incremented by 1 second as upload retry does.