after a couple more reboots things seems to be working fine again.
Didn't do anything special, simply I waited a full day before rebooting again. Maybe the nightly Update_Packages.sh settled everything.
Now I don't get anymore warning related to missing Generic_Pc_as_MD.sh missing, and Onscreen Orbiter is showing again.
Funny thing is that also now I couldn't find the mentioned script in any remote cluster of my HD.
May be interesting to understand what was the problem and what was the solution, so if anyone has some ideas please post it here
Thanks and regards