I suspect something like this is what has happened and prompted this change with using the Marvel branding
It may have just been a clarification of existing rights, with both sides agreeing what is or is not off limits.
That said, if Universal is building a new Avengers ride as rumored, there are potentially two issues with it:
1. It's not clear that Uni would be able to automatically use the MCU versions of the characters which they might be seeking to do. Some argue otherwise, but I think that those specific representations would not be available without a new deal. (My point with that is could Uni use the Fox versions of the X-Men or Fantastic Four without negotiating with Fox? If not, why could they use MCU characters without negotiating with Marvel Studios?)
2. Regardless of the version of the characters used, the Uni contract does not seem to allow them adding characters at this point. The contract has provisions preventing other theme parks from using characters in the "family" of characters Uni is using, but seems to indicate that Uni is limited to what they are already using at this point. So, if they want to use Thor, Iron Man, Hawkeye, Black Widow, et al. (in addition to Captain America and the Hulk, who they can and do use), they might need new permission from Marvel/Disney.
Point being, it's possible that Uni did have to "get something" for their own plans for Marvel.