Strangely today for the first time in many boots I did not get the emergency mode message and the boot went just fine, so for now I won’t be doing a fresh install. It leaves me just with a couple of minor issues, one being this weird flash not working in Firefox (but works just fine in Chromium) and the other the pc microphone volume control missing on the volume panel indicator (Ubuntu MATE 18.04 missing microphone volume control in panel indicator) which already happened on a previous installation of a 18.04 beta. So no big deal, no major issues.
Thank you very much for the help.