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Good question! I never tried but it might work. Since I replaced some Pokemon in Rocket strike, I could think that those shouldn't be transferred, though.
There are already a couple of Team Rocket hacks but this is the first hack where you're part of Team Magma (to my knowledge). Good luck with your project!
To be fair, I remember that in the past if too old threads like this were bumped then they would be closed by moderators. That rule changed sometime. Nevertheless, I wouldn't count on any progress here as well :)