It seems that a few folks over at XDA have found themselves in an unfortunate situation after having accepted the 5.1 update on their Nexus 6 and flashing an older rom. Some roms automatically flash bootloaders and radios to ensure that all rom users have the same experience overall. This is done mostly for debugging purposes. If the developer knows that all users of XYZ rom are running N bootloader and E radio then they can rule out an old outdated bootloader, and focus on the issue at hand. This has been a pretty widely accepted practice for Rom developers to include this auto flash in their install scripts.
This practice also caused a few Nexus 6 bricks. Apparently due to the new security features in 5.1 you are unable to flash back to a previous bootloader. Once you have flashed the 71.08 bootloader or any newer bootloader, attempting to revert to an older bootloader places your device in the Qualcomm bootloader mode. Since it was discovered that Cyanogen was causing bricks for those who updated the Cyanogen has actually changed the way the installer works for nightlies going forward. The installer includes a check that will make sure you are running a compatible bootloader. It will flash the rom only unless it sees that you are running a compatible bootloader. If you have managed to brick your device head to the link below for the fix.
via XDA