If the sync is good and your notes are preserved, you can continue as normal. I'm not sure at this stage whether the server will have been updated with a newer blank database and will therefore overwrite your old files again. Go to Tools > Options > General and re-set the custom folder destination.Copy your original database folder from its custom folder to your desktop.
I can imagine that it would be possible to recover the notes from that 'other' database with a little care, but please don't do anything without checking with Evernote first - they might have a different fix in mind.
You mentioned having the database in a custom folder, and it sounds to me like the updated Evernote simply installed itself with the standard folder set and created a new database, so didn't 'see' your existing notes.
I have now found the version from which I updated: 5.
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