Two things have changed. The file format changed, first of all, so older maps may no longer be recognized. Secondly, the directory has also changed.
To solve the first problem, you'll need to find the file converter that updates old map files. I'm not sure where it is; try a search in the modding forum.
As to where you should put the files, the new directory is C:\users\<username>\AppData\Local\Ironclad Games\Sins of a Solar Empire\Galaxyforge
Hope that helps.