At one point I even deleted the toc.ncx file entirely from within the editor and then had it make a new one. There are no red markers on any of the links. I used Kobo Utilities' "Update ToC for Selected Books" to send a new copy of the book and then the new ToC to Kobo. I'm beginning to think it's an issue with Modify ePub. Maybe I'll put a link on the plugin's page back to here about it.
I've made a scrambled version of the book:
https://drive.google.com/file/d/1fHz...ew?usp=sharing