Hey Kenny,
As I'm sure you know, AF is a water based stain. If you don't get all the water-proofing Permalyn sealer off, then you may end up with a splotchy coloration when you reapply.
Some other stains can penetrate some types of water-proof coatings. You may want to consider those as well. You might still want to strip the sealer first, so as to get closer to the base layer of wood. But if a bit of sealer remained along a molding or in some carving, it might not matter with the other stains.
There is a whole lot on here about stains and finishes. You can use the search fuction at the top to review old posts.
You might also want to explain more about why you are wanting to do this. What is the situation that you are hoping to change/rectify/fix? That would help you get some more specific advice.
whetrock