You should be alright to use an emulator. The only thing I think would change would be load times, and those are eliminated by our in-game time calculations. This is also the first time an emulator has come up, so I'm excited to see it to be honest. Good luck!

The Pokemon LBs have rules that state which emulators are valid, which I think right now is only Gambatte.  I believe they even have a version of Gambatte that they want you to use that might (big might, I don't know for certain) be available for download under the Resources on the boards.

You can check there for the emulator and ask the mods if you have any questions about it.

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