Flattening means several quite different things for PDFs. At least two of them apply specifically to your case, and with printing there is too much at stake to guess; I would advise you to ask the following question:
"We've been told that flattening could mean
- removing transparency effects
- combining layers into one
- making sure comments and form fields are part of the background (probably not relevant).
Please let me know which kind(s) of flattening you need - transparency and/or layers.
Also, do you need a particular version of PDF (e.g. PDF 1.4) or of PDF/X (e.g. PDF/X-3)? It would be helpful to know why you have this requirement."