I didn't think it was exactly what you were looking for. They're still the same characters, but they have multiple status afflictions, can equip nothing, and appear to be equipping helmets. And they have Epoch's portrait and stats.
Hmmm... this is interesting. I got curious and downloaded the save state to check it out to see what this was all about. It turns out that in the first fight (with Gato) they both had 'Stop' and 'Poison' and later on, after being either hit by or had evaded an attack, they only had either the 'Lock' or 'Confused' ailment. After Crono won the fight (he wasn't confused), I went to Crono's house and decided to take a nap at his bed and restore their health (as they barely won that fight from the poison, which for some odd resaon had like a 45% decrease rate).
Then I decided to check out Guardia Forest and see if they really always had the status afflictions. But to my surprise they were all gone! So, my question is: Has any of this happened to any of you guys already? I mean, were you able to get similar results?
Oh and by the way, they were both able to damage the Hetakes in Guardia Forest. Crono was doing regular ** attacks of 700+hps and 1400+ critical ones, while Marle was stuck with ridiculous 5hps normal and 10hps critical hits (I think this is because her hit stat was only 1. Oh, and Crono's speed stat was the one stuck with 0).
Edit: Wow! This is really cool! I played around it with it some more... it turns out that they both have access to all of their techs! But they only appear in the battle menu. I tried using Luminaire with Crono, and Haste with Marle. 9999 on all enemies, of course! Oh, and all of their double techs are still there, as well.
Also, I forgot to mention what their max MP value was: 55 MP for both of them. The odd thing about that is that, in battle it only says that they have 5 MP (using any tech really messes this up as it can actually display Crono's sword icon). I can't equip anything on them either (its almost as if the menu coding of the game just isn't working right), although they do both have helmets as their weapon (not in their equipment). I can, however, use items (like Tonics) through the menu, so obviously some parts are still working. Regarding the battles, they yield neither experience nor tech points, but they still offer items for spoils. Well, I hope that was everything this time. This really makes me wonder as to what Lucca's messed up stat value is going to be (probably the hit stat, just like marle).