this sounds a lot like the symptoms caused by your mirc.ini vanishing, which is most likely caused by a bug that should have been fixed around version 6.3, or caused by your antivirus deciding to quarantine mirc.ini, or windows crashing mirc right in the middle of a disk write to mirc.ini
when mirc.ini vanishes or gets filled entirely with ascii 0x00's, mirc will rebuild another one from scratch using the default settings. your aliases would still be there, because if you're using the default name aliases.ini, mirc.ini will know to open that file to show your aliases. However, all your remotes scripts are listed in the [rfiles] section of mirc.ini, and a brand new mirc.ini wouldn't have that. your server definitions are kept in servers.ini, so would still be there, however the settings of which networks to connect to and whether to autojoin them, would be settings in mirc.ini that are now refreshed to the beginning.
Any address in the users tab of alt-r window and your variables tab would still have all your variables, as long as you have been keeping them in the users.ini and vars.ini that the default mirc would be looking for.
You should be able to use /reload -rs name-of-the-scriptfile.mrc
to load each of your remote scripts into the REMOTE tab of the alt-R window, though it might be a good idea to actually use your scripts' normal install procedure because some scripts at install are making sure your mirc settings are adjusted the way they like, and some of those might have been reset to defaults by a fresh mirc.ini
I used to see this bug happening for some people in older versions of mirc, caused by windows crashing in the middle of a disk write to mirc.ini. I don't know if it's a coincidence or not, but it seemed to be less likely to happen when someone was able to shrink the size of mirc.ini to be less than 8 KB. The easiest way to do this is use Alt-J to remove some of the default channels that you know you're never going to use. i.e. #windows95
