Say it was a Darmanitan. Will it dissapear, or will it just not be registered in the Poke'dex?
You can't, it's impossible, Pokemon can be migrated from 4th gen to 5th, but not traded.
Source: Multiple websites, including numerous Q's on the db, and I've actually tried it
It's impossible, if you trade Pokemon from Pokemon DS games (before B/W) it says if you trade these Pokemon, there is no way to get them back. So it's impossible.