File does not save.

Well after trying to troublshoot and search online, I found that "Resource Updater" is your best bet to resolve the issue. I guess certain resources such as Materials, Alphas, Filters, etc, in Substance Painter get "Outdated" some how and they need to be updated. You can access Resource Updater on the left side in the same colomn as the Brush and Eraser icons. In there you must select Outdated in the dropdown menu. That will populate a list of any and all resources that are outdated. I hope this may help others as well.