The uninstaller, uninstalls the last version you installed
FE: if you installed the mods version first, it will delete the updates one
Anyway, (as i said), you can have a online/updates version & mods in just 1 installation, just install the patch in Mods, when you want to play with patch, change Load
line to the name of the patch. When you want to play online or with default version, just change the load line to <None> (All of this in Mods.ini).
You can update the game without hurting the patch, just install it in Mods
Hope you can understand