Try this
1. Use ungreedy (.*?)
2. Treat the whole string as one line. use /s

my ($new_source) = $source =~ /<!-- InstanceBeginEditable name="guts" 
+-->(.*?)<!-- InstanceEndEditable -->/s;
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instead of

my ($new_source) = $source =~ /<!-- InstanceBeginEditable name="guts" 
+-->(.*)<!-- InstanceEndEditable -->/;
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