Thanks, but I cannot help you there. I have never mixed records with someone who has cheated. I will assume that you are safe since there is no actual Pokemon exchange. When you mix records, the following things happen:
1. You get the quiz lady in Lilycove that they had.
2. If they had a Secret Base, you will now be able to visit that location and battle the Pokes that they had on their team when you mixed records, once per day.
3. You can register their SB so that it will never get over-written by subsequent record mixes.
4. Your Trendy Phrase (NOT Feebas locations) will be changed to theirs.
5. You will get the Mauville Man that they had.
6. Your Battle Frontier Record Hall will reflect their accomplishments too.
7. If you have Pokes in the Daycare with mail and the person you are mixing records with does too, the mail will be swapped.
You could be safe, but then again you are accessing Pokemon info when you battle in their SB, so who knows. That is just one of MANY reasons why it is stupid to cheat. Not only do you compromise your game, but it really destroys the fun out of the game completely. Friends don't let friends cheat.
If it were me, I wouldn't mix records until your friend resets their game and clears out any traces of cheating. Hopefully their cart isn't corrupted to the point where that isn't possible.