The current concept of priced files with tiers is an abomination in it's implementation. You are right to complain to itch and to the developer about the situation.
While some might take issue with the word, what we have here is basically paid dlc. You bought the base and extras. Now you suddenly no longer have access to the extras. Selling extras via a non increaseable tier level of donation is wrong. Even if you wanted to, you cannot increase your current payment-level. You would just buy the whole thing again. The current system is very ill fitted for changing prices. Or bonus content in general.
Reducing clutter projects that are just extensions of an existing project is a good idea. But in this case it would have been the wiser decision to make separate projects, since the current system actually cannot sell more than one item per project page. Not with a returning customer wanting to get the bonus content. It only works if the dev never changes prices, and the customers never changes their willingness to buy bonus content. It is a bad situation for developers too, because if they want to increase price, that might be a bad idea to alienate their existing paying customers. This is an easy way to get negative comments and ratings.
The most elegant fix for the situation is the most needed ability to increase donation level. Seriosly. Why is this not possible?! If you have already purchased something, it should ask if you want to gift the game or increase your donation, not just make you buy the thing again. Or, of course, a functional system, to sell additions to a project, that are henceforth marked with the bought status, just like the game will be, if prices change.