I'd be perfectly fine with them retconning YIJ. When I watch that show, I really have a very difficult time seeing the character as a younger version of Harrison's Indy. The personality and attitude is just so completely different. And, I know this may sound like a trivial complaint, but Flannery's voice is completely wrong. Harrison's Indy has a strong, authoritative voice, and Flannery's doesn't. Again, it comes down to the attitude, I guess, since the attitude is reflected in the voice. If we consider the fact that the Indy we saw in TOD is the closest in the timeline to Flannery's Indy, it simply does not line up at all. Totally different character.
So if they can come up with a new Young Indy that feels more connected to the "real" Indy, I say go for it. I'm not saying he needs to be a carbon copy of Harrison's Indy, since people DO change as they go through different experiences, but it needs to feel more believable that the Young Indy we're seeing has the potential to eventually become Harrison's Indy.
(A friend once pointed out that Flannery's Indy seemed more closely related to Michael J Fox than Harrison Ford.)