Im using JPEXS to edit an SWF I obtained of MutilateADoll2 that is Site locked (referrer) to the kongregate website, is it possible to.... per say... Remove that referral lock and gain access to use the swf offline (via embed)
As described in the comments above, even given that your intentions are perfectly noble, this is a publicly visible site. If we told you how to defeat a game developer's protections on their game here, any bad actor could come along and use that information to rip off our fellow developers' hard work.
So, I hope you'll understand that many users of this site would find it unethical to post an answer about how to defeat this type of protection.
So, instead of "how can I remove this protection", I'd recommend we approach this question from the direction of "how can I obtain a version of this game that works offline?"
Here, the best approach we can offer you is to contact the game's original developer, eg. via their Twitter account, and ask if they would be willing to share a non-protected version with you / grant you a licence to use their work in the way that you describe.