Pencil eraser is the best thing - can't do anything wrong with that.
As for the HxC floppy emulator thing: I think it just proves that it's not a proper emulation. It works with real drives (to my knowledge: all brands), and that gives a hint at "we're seeing a problem after installing the ACA500". Note that this does not say anything about causality - the problem has probably always been in the floppy emulator, and it's showing only now that there's the slightest change in timing behaviour of the A500.
Besides, the floppy emulator is not really needed any more if you have an ACA500 - a real floppy drive is good enough for the few times that you ever need the drive. To stay with the car metaphor: There's no need for a cassette adapter for your portable CD-player if you have an MP3 player installed.