Strange behavior creating and deleting event flags

I'm working with a simple project for the EK-RA6M3 evaluation board.  I've been working with Synergy for several years.  I created a simple 3-thread project for the RA6 and started adding event flags.  After adding three event flags, I added a fourth and noticed that it was not added to common_data.c or common_data.h.  The first three eventflags were still present in those files, though.  I added a fifth event flag and it also didn't show up in common_data.c or h.  I deleted all 5 eventflags, deleted common_data.c and h, and regenerated the project.  The common_data files were rewritten but they included the three original eventflags, which I had deleted.  I killed and restarted e2 studio, erased the common_data files, cleaned the project, and regenerated the project.  Again the three original eventflags are still present in the common_data files.  I see the three original eventflags are still present in configuration.xml even though I deleted them in the Configurator.

Please advise how to regain correct eventflag behavior.

Thanks

tom