I'm new to qubes but in my seaches to get up to speed (seems like I'll never 
see the light of day again after starting down the Qubes rabbit hole!) I 
noticed this post and when researching what AEM is found this on the Qubes 
website:

o - If you are using LUKS with LVM, you must encrypt the whole volume group
    instead of each volume, or else AEM will fail to boot.

Could this be why your AEM no longer works? Just a thought, disregard if not 
applicable. That same qubes web page also says AEM requires legacy boot, which 
I will not use. Shame, AEM sounds useful, tho I suspect UEFI may be better. NOt 
sure how TPM fits into this yet, one more thing to find out about. My mobo 
supports it being bleeding edge new.

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