(I am a high school teacher & no Canvas expert. Here is my experience.) Last year I tested this out: I had a student use the Canvas Student app to annotate a PDF embedded file (Submission Type: Student Annotations) in an assignment. Once turned in, the student could see his submission and my annotations I made on his 'paper' in the Canvas Teacher app. However, his PDF link was now the original blank (unannotated) document. Student would have to start from the beginning.
The only thing I could figure out was to make/encourage students to download the file (via a file link in the the body of the assignment) to their device and annotate in an app. (We use iPads, so either in Files app, choosing 'on my iPad' (iCloud files glitched), or in Notes app). Students upload their annotated files into Canvas, submit assignment, and still have their annotated copy. Some students will take screenshots and use Photo app to annotate. Students see my annotation on their submitted copies as long as the assignment is open.
I don't know how this works with Google files or with files plugged from Google Drive (LTI).
