2.0 in-application updates leave the install alone, keeping updates elsewhere.
The 2.0 plan used the install as a launcher for latest version, thus no reminder.
Wrong how and when? Barring bugs and fallout from the mishap, I’d have thought installing 2.1 would produce a shortcut to its newer Duplicati in its normal location.
Some things can be deconfigured, e.g. start at login, but I think menu is mandatory (I’m not an installer dev, but you’re also talking to someone who seems to know it).
If you mean old shortcut to 2.0.6.3, its date could be checked for hints as to maker.
If jobname means random letters or digits, they might be job database backups.
Generally these are not useful for long, as they get obsolete quickly with backup.
To be super-safe you can rename, but you checked all the files, so likely no worry.
If you have other jobs, it might be safest to at least sanity check health a little bit.
Unless you have to do things like connect a drive, Verify files takes seconds.
This will update the job database version (probably leave a new .bak file), and do some DB self-tests, and probably about three file downloads from the destination.
Your inspection and one backup seem good, some perceived worries might not be abnormal, given the 2.0 design (old shortcut is a mystery), so you’re probably fine.