perfectlymarvelous,
Definitely let us know your experience and how it turns out.
We also have tickets for one of the newly announced Munoz performances, and as good as he was/is, one way or another this production definitely won't be holding on to our money for them... mostly because we already saw the show at the public and, as it turns out, it happened to be one of the performances Lin-Manuel decided to sit out the day beforehand to "watch the show" (although he was nowhere to be seen in the audience that night).
As much as we truly loved the show (and Munoz), the main reason we purchased tickets again (and at Broadway prices) was to see the Lin-Manuel performance we missed off-Broadway. By announcing the alternate not only after performances have begun, but four months after tickets went onsale, the production is risking a lot of good will with ticket holders to those performances he now won't be playing.
"Shady" is right. Or so it seems to me. But shady or not, on a certain level the production really will have to accommodate exchanges or, at the very least, hassle-free refunds.