Thanks for the suggestions guys. I was able to fix my model. Sadly the script didn't work because the subsequent removal of faces broke some other faces (not the fault of the script - probably the geometry of my object). But I was able to delete the round edges and rebuild them with the help of lines and the planar feature. And I remembered to save a backup without filets this time :)
One other thing I learned. Sometimes when I create filets, they look broken because their size conflicts with the adjacent edges. If I go ahead and accept the "broken" filet, then I can still make it work by selecting the model and the broken filet and doing a boolean merge. Then I can delete the additional remains and have my filet.