6 years later and in Pro I'm also getting the 00068 error. My script creates an intermediate table using the in_memory workspace:
arcpy.CreateTable_management('in_memory', 'outTable')
Then the script does some things to populate the table, then copies the table. The in_memory/table triggers the "broken project data source" but the table is not a project data source. It's created by the script!! I save other intermediate outputs into the in_memory workspace as well, but these do not trigger the error.
Any ideas? So far my attempts at a work around have failed.