I have 93 pages with 93 spreads in one file. I've tried manually getting rid of each new section (i.e. by unchecked 'new section') but that hasn't stopped my footnotes from restarting every few pages or so.I have CS6.
You say it is all one file, but is it all one story?
If you want numbering to restart within the document, select this option and choose:
- Spread, or
to determine when footnote numbering is restarted.
Otherwise just untick "restart numbering every"
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