The reason why he wouldn’t do that was because he thought it was “too much after Monica and Chandler”. While part of me is still upset he denied that offer, I also get why he did. It was only 5 years after Friends had ended and she asked him to be her boyfriend on the show, so naturally, as people still remembered them as Mondler, it would a) be the same roles they’d be doing - a couple, and b) it would end in a bittersweet way (their characters would’ve just fooled around and broken up again). So I think it was during a phase in his life where he just wanted to move on from Friends and do different roles; something that wouldn’t remind people of Chandler (and Monica). Plus, he might have wanted to keep that nice picture of Mondler we have (them happily married with kids) alive and not ruin it.
And if it had something to do with true feelings, we might also consider it simply being “too hurtful” for him to be around her in that way again.