Oh, Word. It appears “It just works.” then betray me at the very last moment.
The cross-reference and Track Changes do not get along well. I figured out that the numbering may not be correct/updated till accept/reject all changes. If you want to keep the previous changes, you are in trouble. Track Changes seems to be meant to track changes ‘once’.
What is Track Changes in Word?
If you want to keep track the history of the changes, this plugin may help.
Version control plugin for Word
p.s. The numbering and formatting of the citations does not seem to work correctly. I just don’t have a gut to touch my proposal to figure out what is wrong. It will be easier to go back to LaTeX.