They are backed up. Since Enderal doesn't require them. Also it's been advised, you install Enderal on a clean install, or a vanilla skyrim profile. But then again you might have known that, if you read the installation instructions. About your dlc's, they will be put back if you uninstall Enderal.
Edit: about your downloaded mods, if they require DLC, they won't work. Or they might work but not as advertised. Search this forum, for a compatible mods list. Also I unistalled every mod I was using prior installing Enderal, then ran the game to be sure it worked. Then I re-installed some mods which were compatible with Enderal.