Originally Posted by eNGiNe

Speculation, but would one possible workaround be to stop using the balloon comment mechanism – since this doesn't let you work with files in different versions – and use styles instead: one style for "input from editor" and a second style for "reply from author". Use the customised ToC options to round up just the comments; use search/replace to remove all the comment threads from a finished document, or even update the styles to "hidden" to maintain an archive.