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Filesystem Gremlins?
IIRC, there's a fallback in place for read-only filesystems (because external SD cards and Android, or something), which might have explained why the settings would have stuck, but I don't quite remember how said fallback works... ^^.
(Because, otherwise, the answer to your question would be "everything document-specific", short of some part of the document's metadata which is duplicated in an SQLite DB for the FM the first time the file is browsed).
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