What tool/method are you using to flatten the file inside of Acrobat?
Also, what version of Acrobat are you using?
I have tried a couple of methods in Acrobat, including the transparency flattener in print production to name one. All methods lead to my transparency going black, except with Acrobat print to pdf, however this has its own issues with some of the pdf files that I am using.
It is very frustrating that this can be done with one click of a button in other pdf programs, however it does not appear that Acrobat DC has the functionality, let alone easy to do! I have also tried the same with Acrobat X and this is proving no more useful. Hoping someone more familiar with Acrobat can provide some insight.
You can flatten the annotations using the preflight profile "Flatten annotations and form fields" .
1. Open the PDF and choose Tools > Print Production > Preflight in the right pane.
2. Select the profile "Flatten annotations and form fields" under PDF fixups section.
3. Click "Analyse and fix" button.
Hope this helps.
Is there a way to flatten annotations without flattening form fields?
Set all form fields to be non-printable and then specify the nNonPrint parameter of flattenPages to 1.