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Root Going back to stock rom then flashing Android M

Hi, I have a Nexus 9 that I would like to restore from CM to stock lollipop then update to Android M. I am concerned though that when I upgrade TWRP will get in the way. I might also do some old lollipop updates since I moved to CM right when I got my nexus 9 in January and 5.0.1 sucks haha.

Thanks!
 
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