The custom project did not load into the project list after restarting. This time SQX did not previously crash I just restarted SQX normally and the project was gone from the list. The folder still exists and the project file too.
If start getting this error upon updating any settings in any task then after restarting SQX the workflow is corrupted and gone from the list. I still don't see a pattern to reproduce it exactly, it just happens sometimes.
EDIT: It can even happen without changing any settings, just clicking from one task to the next.