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I'm looking at a firmware dump from a NAND flash chip and comparing it against another similar firmware dump I have. I am able to open one of them to see the root folder structure, however the other I cannot.

The one I cannot has these "random" 40 bytes of 0xFF strung in, which I think isn't allowing me to extract the filesystem from. I believe the root folder structure should be similar, if not the same as the other firmware dump I CAN open.

Is this a case of non-standard compression? How should I go about opening up these file systems?

I can upload the firmware, but they are 128MB each so kind of large files.

Here's a beyond compare between the two. The unknown on the left: https://imgur.com/dfEtGEI

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Do these extra bytes appear at regular intervals? If so, they could be the spare or OOB(out of band) bytes which are present in most NAND chips for error checking or housekeeping (bad block management etc.) in most cases you can discard them and analyze just the “useful” data. See my other answer for some background.

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