When I open my projects, I see the Stylesheet listed as usfm.sty and then off to the right, it says (Customized). I'm assuming you're seeing something different, probably something with a different name instead of usfm.sty.
If you close PT and open the Settings.xml file in the project directory, then you should be able to manually change the stylesheet name. I think if you name it as usfm.sty (and make sure that file isn't present in the current directory, then it will look for usfm.sty in the My PT # Projects folder one level higher, and also use custom.sty.
You would then need to port the necessary styles into custom.sty. This can be a little tedious because in general you only want to list places which change usfm.sty, whereas your old customized stylesheet probably had lots of places which just copied the default values in.