How can I adjust a skeleton for animations?

Hey guys I’ve currently retargetted the animation starter pack animations to a new mesh/skeleton of a model. I’ve set the root and pelvis to animation scaled and the rest to skeleton. The problem is the animations are very off with this retargetting, and I can adjust the skeleton while previewing the animation to get it to look good. The problem is I can’t figure out how save these changes, if I open the animation sequence or reopen the skeleton it’s back to looking wonky.

I’m wondering if I’m missing something? I don’t want to be modifying bones in blueprints and would prefer to get everything looking good before gameplay. The first screen shot is what it looks like wrong, and the second image is what I adjust it to (but it isn’t saved). Any help would be great. Thanks!