allowPageShuffle
var myDoc = app.documents.everyItem()
var mySpread = myDoc.spreads.everyItem()
myDoc.sections[0].continueNumbering = true;
mySpread.allowPageShuffle = true;
var myDoc = app.documents.everyItem()
var mySpread = myDoc.spreads.everyItem()
myDoc.sections[0].continueNumbering = true;
mySpread.allowPageShuffle = true;
If I understood you correctly, you want something like this:
var section,
doc = app.activeDocument,
sections = doc.sections.everyItem().getElements();
for (var i = 0; i < sections.length; i++) {
section = sections[i];
if (!section.continueNumbering) {
section.continueNumbering = true;
}
}
doc.documentPreferences.allowPageShuffle = true;
doc.spreads.everyItem().allowPageShuffle = true;

You don't need to reference your documents like this:
var myDoc = app.documents.everyItem()
You can reference the current doc either
doc = app.activeDocument
or
doc = g.doc (the reference to the current doc sent from the batch processor via the global g variable).
Note: there is already a very similar script (I just added a couple of lines and removed an if statement).
Hope it helps!
— Kas
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