Let me say this right up front I'm not taking any sides here what so ever .
and don't know either person in this .
but drilling a little material out of a flex plate for balancing a engine will not affect the SFI cert. now if you have altered it by enlarging the converter holes or by drilling through the flex plate or some other type of altering then it would not pass SFI spec.
And i have run all over the place and have never had a tech person check a flex plate i have had them check the trans shield a few times but never the flex plate or the damper.
I could have just been lucky i don't know and I'm not sure that i would even buy a used flex plate to start with .
I'm not trying to pee on anyone just thought i would offer that little bit of info.
and it is only my opinion .
Have a happy and safe new year