How to update the Nexus 6 to Android 5.0.1 with encryption off+root with no data wipe or loss from rooted 5.0
Download & unpack the Factory Image to your Platform-Tools folder.
Boot into bootloader
fastboot devices to be recognized
fastboot flash bootloader bootloader-shamu-moto-apq8084-71.05.img
fastboot flash radio radio-shamu-d4.0-9625-02.55.04.img
fastboot reboot-bootloader (don't skip this step)
fastboot flash boot boot.img (this one http://goo.gl/l1YDn00
fastboot flash system system.img
fastboot flash cache cache.img
boot to twrp
If you were previously rooted you will maintain root after reflashing the SuperSU file. The modified boot image with encryption off is linked. Use the original to keep encryption turned on. Enjoy!
As always, it you have to ask questions about adb, fastboot, drivers, etc, you probably shouldn't attempt this and I'm not responsible.
Edit: not sure who repackaged the boot img to give credit to, but thanks!