Are the metadata stored in S3 or Glacier? Can you choose to recover only particular files? Then you can use Glacier not only as a last resort backup, but also as a defense against bit-rot if say one backup fails and the other is corrupt.
(I'm the guy behind Arq) The backup record data are stored in S3. Otherwise it would take 4 hours just to look something up, which would be unusable. You can choose to recover individual files, just as before.