You have forgotten an important detail: i have tried to manually edit the file and i can really write it and it is rewritten after device boot.
I have done a check disk on it also and got no errors.
I have made this test:
1- I have a copy of the manually modified media file (with yesterday date). I delete the media.xml file on the reader, take a copy of my modified backup file to media.xml (which is now yesterday date). Than i compare the backup and the media.xml. They are the same dated from yesterday. Then i safely remove the drive, shutdown the devices and after restarted the media.xml has been modified to the reader and becoming different from the manually backup file i used few minutes ago. I can see also that the new media.xml file after reboot has the date/time matching when it was rebooted.
The file "cacheExt.xml" is modified also on the reader after reboot...
I have tried to power up without PRS (usb plugged) and it changes nothing at all...
Conclusion: media.xml file is rewritten with old date data from my 3 choosen books by the reader itself !!!