What cart do you have that you need an AP removal patch for a 2012 vintage game with it? Might be time to get a proper cart.
Anyway stacking patches varies with what is done. If the AP patch is done properly though then it should stack with the other.
The problem in this case may come with xdelta. Unlike a lot of earlier patching systems it tries to verify the input file is the one it expects, and obviously if you have changed it with an AP removal patch then it will not be what it expects. Xdelta's command line does have an option but if you prefer a GUI then
https://www.romhacking.net/utilities/704/ should have it too.
Do the AP one first as it should change very little but the remaster patch will probably change things quite a lot and might confuse the AP stuff.
The AP patch if done properly should take out the relevant binaries and overlays, patch out the AP checks and put it back in exactly where it found them. Not all will and I don't know the DS-Scene tool well enough to know what approach it uses. If necessary we could take the AP patch, figure out the changes and insert that back into the ROM and disrupt as little as possible such that it won't matter. Hopefully it won't come to that though. Alternatively we could merge the two patches at file system level but that is a lot more work.