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I just tried in Evince and you can print an annotated document to flatten it just fine.

Can you show me how?

I'm using Document Viewer aka Evince 3.28.2 on CentOS Linux release 7.6.1810 (Core) and I don't see an option to print the PDF with annotations.

It's just the normal print option. Fill out the form, Save As with the form filled out (not sure if this is necessary), print in the main menu