I have the same issue. All my 98 run configurations ARE saved in .run The run configurationitself is saved in .idea/workspace.xml inside:

From time to time, this list LOOSES its order, and becomes shuffled, I do not see any logic in the reason when this happens, nor in the new order of the components.

Then I looses 10 mns to reorder the list.

I have tried to restore that part of workspace.xml, this mysteriously fails.

NB: all my tests have a well defined name in the xml file: Python.00, Python.01 etc.