are you really adding hundreds of taxa one by one to the project criteria? it should be possible to these in bulk via the API. back in the day, i asked @maxo how he was making such changes, and he said that he was doing it programmatically. maybe if you ask nicely, he might be willing to share scripts or tools to do this?
although i can understand why the system might refuse to add or remove hundreds of criteria in on transaction, based on my previous experimentation with the API to update projects (https://forum.inaturalist.org/t/edit-project-breaks-entirely-for-project-with-undefined-user/30070/13), it seems like if even a minor change is not being processed, it would be because the screen is sending the API the entire project definition rather than just the changes. seems super inefficient from the perspective of making updates to projects, although i suppose the screen would be easier to code if you didn’t have to keep track of the changes that occurred.
but i guess until the problem is resolved, if you need help making minor updates to a project, and are willing to try using the API to make such changes, i can describe some steps to make the necessary changes.