I was changing up my 4 piece and took the 13 inch rack off and put te 12 back on. The 13 and my floor tom had coated emperors and the 12 in rack tom has stock 1 ply remos. I love the sound I get from this, but do you think they will sound too far apart in recordings.
I guess you can always compensate by tuning.
If you mean too far apart in the sound ( and not the pitch ), then I'd say take a shot. If it will sound good acoustically, then it will do just fine on recordings. At this point I can't recall any, but I do remember reading once or twice about professional recordings with different heads on toms and different on floor toms.
Right now I've got a pinstripe on my floor tom and 13" rack tom, and single ply stock heads on my 10", 12" and 14" rack toms. In all honesty the pinstripes sound the worst out of the lot, and to me they stick out like a sore thumb because they sound so dead compared to the others. I roll down my toms and it sounds like I get two dropouts in audio, because the pinstripes just don't speak like the other heads. So in answer to your question, I would say there would be a noticeable difference (depending on how attentive the listener of the recorded music is of course). But you can compensate, depending on how you record your kit. I would go close miking for each drum so you can make the drum with the different head fit in more evenly through EQ or dynamics processing. And a bit of reverb always helps smooth things out.
I'm changing all of my heads fairly soon, and just going with clear Emperors or maybe the single ply Ambassadors on all the toms.