Makbo,
I also encountered issues in applying tickmarks to protected PDFs which did not allow for editing. After some Google-ing, I learned that the Chrome web browser does not respect these limitations. Accordingly, if you email the files to yourself, open them in Chrome, and print them to PDF, you will be able to edit the resulting PDF files.
If your PDFs are opening in a separate PDF program and not in the browser itself, you will want to adjust the following setting:
Settings > (scroll all the way down) Advanced > Privacy and Security > Site Settings > PDF documents > "Download PDF files instead of automatically opening them in Chrome" and set that to "OFF".
Hope this helps!