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/mnt/ext1 is part of the internal storage. The SD card you insert yourself is mounted at /mnt/ext2.
The configuration files are saved to the filesystem in /mnt/ext1. On some devices, the internal storage was actually an SD card, as well, and that would go bad for some people and revert to read-only mode. In that mode, no permanent changes to the files were possible. It would look like the files were changed while the device was running, but the changes were only in RAM and wouldn't be saved to storage when the device shut down. So, when you rebooted the device, all the old configuration settings would reappear. Indications of bad storage are configuration changes that revert, books that disappear after being copied to the device or reappear after being deleted, the state of read books (i.e. last page read, font size,...) reverting to the old settings,... When these strange events happen, it is probably because the internal storage has gone bad. So, it's good to check that that isn't the problem before trying to figure out what may be changing a file on reboot.
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