I'm rooted with twrp installed. Which one should I flash in Fastboot and sounds like it'll wipe data afterwards?
Just follow the instructions and you'll be ok, twrp and root don't matter for it - it's just changing the kernel/ramfs partition out. You have to factory reset in order for the encryption to "turn off." Normally encryption is forced at bootup on the Nexus 6 (can't be disabled), this just gives you the ability to disable it - which apparently fixes some I/O read issues (as expected from an encryption SW layer I guess).
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