Editable PDF Font Display Issue



Hope someone has some bright ideas. I'm working in a full version of adobe Acrobat on the mac, and the end user is working in a full version of Acrobat on the pc. We both have the same fonts installed locally.
We have a series of template pdfs that they can drop text into. I've added a lock button that makes all fields read only and hides anything we want hidden. The user is then optimising and flattening the pdf.
We have a few issues with the end pdfs. The copy appears to be 'doubling up' - there is only one field in the pdf for them to add copy to, no additional hidden fields. There's a weird issue with ligatures so it's obvious there's two layers of copy (see pic1) - viewing in illustrator allows me to separate them (pic 2)
And finally once flattened and optimised the headline font is also looking wrong, far too bold. (pic 3)
I haven't been able to flatten the pdf in such a way that it shows no fonts in use. As a temporary workaround having to bring it all into Illustrator and convert to outlines.
Is there anything we can do to flatten the pdf in such a way that it removes all fonts without doubling up the copy?
