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Bootloaders using the FLIP protocol version 1 experience some very specific behaviour.
These bootloaders have no option to access memory areas other than Flash and EEPROM.
When the bootloader is started, it enters a security mode where the only acceptable access is to query the device configuration parameters (which are used for the signature on AVR devices). The only way to leave this mode is a chip erase. As a chip erase is normally implied by the ‘-U’ option when reprogramming the flash, this peculiarity might not be very obvious immediately.
Sometimes, a bootloader with security mode already disabled seems to no longer respond with sensible configuration data, but only 0xFF for all queries. As these queries are used to obtain the equivalent of a signature, AVRDUDE can only continue in that situation by forcing the signature check to be overridden with the ‘-F’ option.
A chip erase might leave the EEPROM unerased, at least on some versions of the bootloader.
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