My first thought is that this could seriously risk spoiling the twist unless you put hard safety rails in place, once the Pcs begin to suspect, they will ask.
So do you have good reasons to rock the boat?
There is no problem with using the Ancestor mystery itself.
One way you could use past lives as ancestors is if you let the past lives be just a few ancestors among the many, and be vague enough that they seem like family just like the rest, never confirmed to be past lives until that bomb has dropped. That means you dont let them say anything of import that you wouldn't have any other ancestor say. Let their identity be part of the big reveal.
You could help obfuscate this by having the PC's family be a long family line of tradesmen, so that one would expect many of them to be similar.
Another idea is that there are strangely many ancestors who are nearly identical to the PC, and they know nothing more than what the PC knows (they have been reset as well!), they can comment only on what they did differently after the event has already passed.
Personally though, I wouldnt risk it. The twist is already good, and hinges on the right amount of secrecy.