Go to Tool menu > Print Production look for Flatner Preview, see if you can flatten from there.
// Flatten all pages in the document
Once you've done that, restart Acrobat Pro and you'll find the "Flatten" option in your Edit menu. VERY handy! Tip: might want to save your original PDF file as a different version just to be safe---once you flatten the PDF, it can't be undone, so either just print and don't save, or save as different version if need be.