I think what happens is that onedrive converts the .doc into an internal format so you can edit it then when you copy it back it converts that internal format back into a .doc file.
You can probably work around this with --ignore-size --ignore-checksum.
This isn't ideal though!
If you are doing this sync regularly then I'd probably do one with --exclude "*.{doc,xls,...}" and one with --include "*.{doc,xls,...}" --ignore-size --ignore-checksum