Can't delete apps that are no longer available in App Store
The apps didn't have .ipa files in my system, which may have been part of the problem. What I ended up doing was a search in iTunes (the global search at the upper right corner of the app) for each one. In the results, there is an icon with three dots, clicking on that icon brings up a contextual menu with the option to delete.

That error message I was getting before no longer appears after that.