by lost their scripts do you mean that the mrc files are not loaded, though they exist in the mIRC folder?
you can use the backup mirc.ini to read from and reload the remotes and any aliases (except the one alias.ini which if you allowed it during update, would be erased if you didnt rename it first)

the option to not replace the mirc.ini for one, would have saved you this trouble

what we might expect backup to do
save alias.ini file
save all popup.ini file(s)
save all remote files (user group so on)
save any mIRC ini files such as mIRC.ini URLs.ini and so on
might make a good suggestion to have mirc scan the mirc.ini and back up all relative files.

might make a good suggestion