Your changes to the Execution Plan would be saved to the Project.mds file, so I would recommend comparing your local file where you made the changes vs what is in the repo branch used by your pipeline. Maybe you are referencing the wrong branch somewhere?
If, by chance, the change that you are checking in is just a "reordering" of the tests in your Execution Plan, those changes may be arbitrary if you are using tags [see here]. You can try enabling/disabling a test or two in your Execution Plan then commit/push changes to see if they are applied.
