It will be OK to format the builtin storage. Formatting the drive does not affect the firmware in any way at all. Make sure to shut the ECOReader down and restart after the format - this allows the firmware to build certain directories on the drive ready for use.
You will LOSE all documents & books etc that are currently on the ECOReader. The standard freebies ebooks are available again at the update link you can get from ECOReader support.
