When I make an assignment submission using an editable PDF filled with data, Moodle stores the original file and I can download it without issues. The problem comes in when I want to grade the assignment. The FPDI plugin strips the text from the PDF and gives me blank PDF without information like the student submitted a blank document. 

Copy from the linked issue:
Steps to reproduce the problem:

1. Make a course with an activity that accepts submissions in pdf format.
2. Enrol the course, set yourself both to Teacher and Student.
3. Get a pdf file that's not protected so you can write on it in any pdf viewer (I tried Foxit 9.7.1 and the latest Acrobat DC).
4. Type any text on the pdf and save it.
5. Upload it as a submission to your activity.
6. Go to grading, find your submission, click Points.
7. Moodle converts the uploaded pdf into an other file and presents a view. The student-made annotations are missing from the view.
8. Still on the Grading page there is a link to the uploaded pdf file. Click on it.
9. Your browser downloads the pdf file. Open it in any external pdf viewer. The annotations will be there.