How can I remove a deleted content file from my book's Table of Contents? I

> I deleted the file ....

How? You need to delete-from-book using the Book menu. A right-click option on the component file name.

> ... updated the book, ...

A necessary step, but might not work if the remove isn't done correctly.

> .... updated the TOC references ...

What does that mean?

I would expect a delete-from-book, followed by an update-book, would suffice.