Corrupted fonts after "Edit PDF"

Every month, I have to duplicate and edit a document that was originally created in Acrobat Pro DC. The document uses the same fonts every time, recognized in Acrobat. Sometimes after editing, the fonts become corrupted- with letters either disappearing or turning into little boxes. The only fix I've found is to go back into "Edit PDF" and change the fonts, then save again. 

It's a real pain, and I don't know why it happens. I've tried Scan and OCR, I've tried selecting "Don't unembed any fonts" in the save settings, and some other fixes recommended by Adobe support, but nothing has prevented this from happening. Should I be working in InDesign instead of Acrobat? What else could be happening, and how can I prevent it? This problem eats up hours of worktime.