It is not just local files that were dropped, all protocols apart from http, https seen to have been.
Also note, there is obviously a huge deficiency in Evernote, not being able to backup the DB! Is backing up the local files good enough when these are synced to the cloud?
More importantly, in this case all the links with non supported protocols are not lost, reinstalling the classic version v6.x from their site restored these for me.
The DB doesn't appear to have changed, and EN's info also implies this.
I'll be staying on classic from now on.