After the LXD snap refreshed to 3.17 I noticed my manual snapshots were gone. I found this in the logs:
t=2019-09-09T07:19:56-0400 lvl=info msg="Pruning expired container snapshots"
t=2019-09-09T07:19:56-0400 lvl=info msg="Deleting container" created=2019-09-07T08:09:13-0400 ephemeral=false name=bionic/snap0 project=default used=0001-01-01T00:00:00+0000
t=2019-09-09T07:19:56-0400 lvl=info msg="Done pruning expired container snapshots"
t=2019-09-09T07:19:57-0400 lvl=info msg="Deleted container" created=2019-09-07T08:09:13-0400 ephemeral=false name=bionic/snap0 project=default used=0001-01-01T00:00:00+0000
t=2019-09-09T07:19:57-0400 lvl=info msg="Deleting container" created=2019-09-07T08:16:41-0400 ephemeral=false name=bionic/snap1 project=default used=0001-01-01T00:00:00+0000
t=2019-09-09T07:19:57-0400 lvl=info msg="Deleted container" created=2019-09-07T08:16:41-0400 ephemeral=false name=bionic/snap1 project=default used=0001-01-01T00:00:00+0000
t=2019-09-09T07:19:57-0400 lvl=info msg="Deleting container" created=2019-09-07T08:09:45-0400 ephemeral=false name=disco/snap0 project=default used=0001-01-01T00:00:00+0000
t=2019-09-09T07:19:57-0400 lvl=info msg="Deleted container" created=2019-09-07T08:09:45-0400 ephemeral=false name=disco/snap0 project=default used=0001-01-01T00:00:00+0000
t=2019-09-09T07:19:57-0400 lvl=info msg="Deleting container" created=2019-09-07T08:16:45-0400 ephemeral=false name=disco/snap1 project=default used=0001-01-01T00:00:00+0000
t=2019-09-09T07:19:57-0400 lvl=info msg="Deleted container" created=2019-09-07T08:16:45-0400 ephemeral=false name=disco/snap1 project=default used=0001-01-01T00:00:00+0000