I agree.
If you make changes to a shared file as a sender and click DONE (which is in the shared comments section and near the sync icon) - it says you can continue to track file activity, you click ok (other option is cancel) and your changes are NOT saved onto the shared file.
if you click SAVE instead, you are told you can save a copy which will not update any additional comments which is not shared.
I don't understand what the DONE button is for and I don't know how to save changes as the sharer to a shared doc.
I suggest:
1. Rename the DONE button as CLOSE SHARED VERSION
2. Add a warning before closing for unsaved changes with instructions on how to save changes or a button to discard changes.
3. Additional colour or graphics in the toolbar of shared version to remind the user to periodically check for updates and syncing.

Our organisation lost out on a chance for funding today because the sharer made changes to a shared doc and lost hours of work. I realise we might have misunderstood something but I do expect these functions to be obvious and intuitive

I agree
If you write onto the shared version and just click DONE - which is the clearest button visible and located above the shared comments and implies the changes are saved to the shared version - the changes are NOT saved to the shared version.
If you click SAVE instead, you are faced with creating a copy where new comments are not added to it - implying the shared document is live and changes you make are saved to the cloud version by clicking DONE.
I cant find a way to work on a shared document more than once as the sender!
I don't understand what the DONE button is for other than close the file.
I suggest:
1. Rename DONE to CLOSE SHARED if thats all it does.
2. Add an "unsaved changes" warning with instructions on how to save changes to the shared file before allowing it to close.
3. Perhaps add some additional graphics or color around the tool bar for a shared document to remind the user to be careful about changes and check for updates from collaborators