Mod path is based on the version of Sins, so when it gets updated by Steam the mod path changes.
Hint:- Use the Options -> Mods -> Show Mod Path button to find the new location, and then move mod folders, such as SOA2R, from the old to the new mod directory.
If the checksum is zero that indicates you may have the mod directory at the wrong level, eg SoA2's entity.manifest would be in
C:\Users\locksquest\My Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion\Mods-Rebellion v1.80\SOA2R
assuming locksquest is your Windows account name.