The reference sensor on the S2 at the flywheel is the speed reference sensor. This is for engine timing. I’m surprised it would run with this not located properly. The engine timing (TDC) is done by the sensor at the camshaft using a metal ring attached to the exhaust camshaft. I will suspect that your shop is not experience at working on the 4 cylinder water cooled cars. Everyone that is knows that the reference sensors project through a hole in the bell housing and MUST be removed before removing the housing to access the clutch. If they are not removed you either break the sensor or the sensor bracket. Looks like this is what happened to you as evidenced by the glue in your photo on the broken pieces. As a minimum, they should have replaced that sensor bracket for you (they are cheap) or TIG welded it together. Now the work must be repeated again to place the new bracket in there.