With 'Track Changes' on, Word may have some nominally-deleted entries that it still has to keep tabs on. Consequently, the reference number assigned to those objects remains in-use. Given their nominally-deleted status, neither those items nor their tags should be displayed.

Re your question, you could accept/reject just those parts of the changes affecting the tags.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]