I'm not sure what is going on with your document but these are the things I would fiddle with to see if something resolves your issue.

Firstly, make sure you aren't revision tracking these changes. It is possible that revision tracking can be causing problems in recording what is being added/removed.

Next, are your endnotes being positioned in regular flowing text or are you adding them to text boxes or tables with text flowing around them? The anchor points of floating objects can cause unexpected numbering on endnotes.

If you are still having problems, I would try converting to footnotes and then back to endnotes. That might resolve the numbering.

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Andrew Lockton
Chrysalis Design, Melbourne Australia