The status of SAP-delivered code really should be in sync between DEV, QAS, and PRD, except for where you have applied Notes or Support Packs in DEV and not yet in the downstream systems. You should not make the changes in QAS. You were right the first time, reset the 'grey' Notes in SPAU in DEV and add those resets (along with all your other SPAU changes) to a transport request per the normal SPAU process, then let that transport request be imported automatically as part of your support pack queue in both QAS and PRD. You need to do it this way in QAS to ensure that the import actually works correctly. If you "do the changes" in QAS to import into PRD, then you haven't actually tested that PRD queue import anywhere. This, also, is how DEV systems get badly out of sync.
The only reason to run SPAU again in QAS is to a) ensure that your transport took care of everything, or b) fix things that are out of sync with DEV because you've been doing it incorrectly in the past.
Regards,
Matt