A sad story: My context-typeset dissertation was printed/distributed by a POD publisher with aweful typographical errors (like all commas in the main font being replaced by an ff ligature).

Horrors, and really strange

Obviously the printer didn't check their results.

The file reads fine both for me and the publisher, but the printer let us know that the file is unprintable due to problems with fonts not being embedded

This is a common problem

(why they originally printed an "unprintable" file I'll never know).

money ?

Now as far as I can tell, fonts are embedded. It was made with context MKII, using hz and hanging punctuation, etc. When I look at the document in Adobe Acrobat, and check the document/font details, it gives a list of embedded fonts only.

Are you sure?
As pable write
pdffonts is very good

I'm not certain that the printer is in the right, but how can I tell? Is it possible that the pdf was altered when transferred from me to the publisher then to the printer?

With very hight probability , no ; pdf is a 'bynary' format
an alteration will broken the file.

That compression of the pdf (zip) had any impact?

With very hight probability , no .

Any other possibilities? What do you need to know to offer advice?

I can send the file or a part of it if it is needed.

yes, if you want .