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I Find and replace enable regular expressions.
If there is only one script tag in each file, using something along the lines of:
Find:
<script>.*</script>
And leave Replace empty
Should do it, but save a copy of the epub first in case something goes wrong.
If there is more than one script tag per file, you may have to limit the greediness of the match to prevent anything inbetween the two script tags from being deleted.
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