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Windows MobiPocket Reader can convert from PDF to MOBI one folder at a time (in library view: import -> add folder). Its conversion is about the same as that from MobiPocket Creator, but you can't edit the metadata after conversion.
Calibre can mass convert PDF to MOBI (add PDFs to Calibre, check the conversion on one PDF then do them all). With Calibre you can correct metadata etcetera before or after conversion. Even if you go the MobiPocket Reader route, you can later import the MOBIs into Calibre to edit their metadata etcetera.
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