This probably isn't the issue you are facing, but worth checking out:
Locally opened files will open to the last used layout. Unless you have a closing script that goes to a "safe" layout, it is possible that yesterday you closed the file while on a layout that references the external file.
I have a closing script that navigates to a interface layout that has no fields etc on it - it's a blank layout with no references on it.
Strange that it just started happening and only on Pro and not on Go.