One of those is invalid, and if I select it, I get an error, but it’s still not removed.
Is it always the second one that gives you an error, or are you never quite sure which one will work?
Yes, hopefully they are consistent. My guess on this is that you loaded a variant of the project at some point, or perhaps saved a copy to another folder. In that case both would be supplied in the menu. I’ll check to see if we have it on the list to disambiguate cases like that by showing the folder hierarchy if possible. This is something that happens “for free” on the Mac, so it might never have made it into implementation notes. Removing an “invalid” project probably wouldn’t be possible, nor desirable in most cases. If something like Dropbox causes the project to cease opening correctly, you wouldn’t want to lose track of it, for example.