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Hi. I never had this problem before. Now all of a sudden when i export multiple pages as PDF's (as seperate pages) a folder is created by Indesign and they are saved in that folder. They used to save in the root folder and not create a new one?
As I recall InDesign always saved the separate PDFs in its own folder.
alternatively you could use Peter Kahrel's Script Batch Process:
( ACP )