Let me explain you. If you use 171117 Pkhex version, and try to emulate the PokéTransfer process, this will happen:
However, when you use this pk7 file with a newer build of Pkhex (21117 is the one Im using), this happens:
You need to change that to "the Johto region" without the (-). That is fixed in newer builds of the program and they will be fine in the next release. It happened to me and now I can freely trade Lugia, Ho-Oh and the doggos.