Bingo!

/lib/partman/init.d/52crypto: IN: NEW_LABEL =dev=mapper=xvda5_crypt loop
parted_server: Read command: NEW_LABEL
parted_server: command_new_label()
parted_server: Note =dev=mapper=xvda5_crypt as changed
parted_server: Opening outfifo
parted_server: command_new_label: requested label with type loop
parted_server: command_new_label: creating

Looks like the culprit right here.  The crypto init.d script is asking
parted to create a loop label, blowing away the already formatted ext4
partition in xvda5_crypt.  init.d scripts are not supposed to modify the
disk at all, let alone reformat a disk that has already been completely
set up.

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https://bugs.launchpad.net/bugs/1523194

Title:
  Can't install /home into separate LUKS encrypted volume

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