Deletion of content that is revision tracked means that deleted content is still 'in' the document. So that deleted content can effect the numbering of items such as footnotes.

If you rejected the deletions and then deleted them without revision tracking that second deletion then you really did remove them so the numbering can behave as expected. Of course you could have accepted all revisions to get the same result.

Whenever you have weirdness in a document, it can be useful to check to see if there are any tracked revisions and accepting them can often resolve the confusion.

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Andrew Lockton
Chrysalis Design, Melbourne Australia