There is no canonical location for an ISBN a PDF file, so where and how it should be stored will depend upon the tools you are using to read it.
There are 2 interesting sources of metadata in a PDF file. The info dictionary, and the XMP metadata. For exiftool these can be accessed by the the 'PDF Info Tags' and the 'PDF Metadata Tags'.
If your tools are looking at a someplace different that you are not modifying (using exiftool), then I would suggest looking at the document in Acrobat / Reader to see if you can find out what they are looking.
Good Luck
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