Hi Barry,
Sorry for the delay. It's actually fairly hard to delete the filters. When you say the filters are "essentially empty" can you tell me which filters are left?

You may be able to restore the filters from Global.mpt. Choose File > Info and click Organize Global Template. Click the Filters tab. Click the Incomplete Tasks filter in the list on the left and click the Copy button to copy it back to your project.

Test and see if that works.