Puzzling about this and hope I can explain it.
I have a Premiere Pro clip within which I expand the scale of the clip to zoom in on a feature. When I import or link to After Effects, AE expands on the expansion if you get my drift. Can I prevent this happening or do I need to do the scale expansion in After Effects instead?
You are talking in riddles and bad terminology, on top of which you are providing exactly zero useful information about things like project settings, sequence settings, effects parameters, screenshots, system information. Given these conditions, it's impossible to make any sense of your post. Sorry, but this is a typical "Ask any stranger on the street and you'll get no answer, either." stuff. You have to be much more specific before anyone can unriddle this for you.
If you're still having trouble, let us know. Keep us informed.