Export and re-import file - what about the comments?

Dear all

This is more or less a work-flow question I think…
I am writing a huge piece of academic work, parts of which I have to send to my supervisor in regular intervals (sigh).
While working on a file (say, a chapter), I find it very useful to add comments (additional to the ‘official’ footnotes) about what to do during revision, what to elaborate on, or what to pick up again in a following chapter etc etc
Now, when I submit a draft, I don’t want my supervisor to read these little… uncertainties.
So I exclude the comments during export.
Then, in Word (trying to get into Mellel, but too stressed out for his right now), I do the formatting. Of course I also find some typos or weird sentences that I then correct.
Then: Bookends for in-text citations.
Done, draft including footnotes goes off to supervisor.
Now, all the corrections and things I’ve done in the rtf. file in word are, of course, not in the original Scrivener file now.
I could re-import the file as a second draft into Scrivener, right, so if my thing comes back with my supervisors helpful annotations, I could rework it in Scrivener (At least I think hat would be a good way to do it, no? Any opnions?
BUT: the comments then won’t be in the new working file!!! Problem! Does anybody have an idea how to optimise my jumbled-together workflow?