Forgot to declare solved the issue. Sorry.
Even if the solution was simple - it is really easy to save your stuff, then perform the upgrading procedure - still would like to understand how could have happened that, playing with the location of the Upload directory, it turned out to have the /mnt/ext/lib, /mnt/ext/usr, /mnt/ext/tmp and all the content in /mnt/ext/etc wiped?
If I'll undestand this I'll tell on this thread :-)
Even if the solution was simple - it is really easy to save your stuff, then perform the upgrading procedure - still would like to understand how could have happened that, playing with the location of the Upload directory, it turned out to have the /mnt/ext/lib, /mnt/ext/usr, /mnt/ext/tmp and all the content in /mnt/ext/etc wiped?
If I'll undestand this I'll tell on this thread :-)