BadgeGen is (originally) a GSAK macro created by Kyle (I don't know his last name). It is implemented by Project-GC.
BadgeGen is released under the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) licence. You can read about it on the link. The important part is the "NoDerivs" part:
NoDerivatives — If you remix, transform, or build upon the material, you may not distribute the modified material.
This means that if Project-GC removes a badge, that would constitute a transformation of the original material which would violate the licence. It could, of course, be done with (explicit written) permission of the creator but it would take that to do it without violating the licence.
I don't see the point of decommissioning these badges. Not everybody started their geocaching career after 2010 and I don't see why they should be denied the badges if they qualify.