All we know is that Jellico swooped in and saved the day!

I guess there is sort of an implication in Chain of Command that Troi chose to wear a “non-standard uniform” until Jellico ordered her to change. He says, “I prefer a certain… formality on the bridge. I’d appreciate if you wear a standard uniform.” I’ve just done a TNG rewatch, and I’m pretty sure there is no other in-universe explanation given.