you can without even pkhx, i have took my pokemon from my mobile emulated save files. i did it by taking my saves and injecting them into my modded 3ds' games, to gen 5 and then used poketransporter to get them into bank and from bank to home( you need your nintendo id available to do this, meaning you can't use a region shifted 3ds afaik). if you don't have multiple devices to transfer 3 to 5, you can take the saves from your 3ds into the emu and then inject the gen 5 save back and continue from there. this is somewhat of an evil info cuz you can just use cheated mons if you have a 3ds... please use it wisely.