I have an annex that I use to store my digital photos. I had a few false starts creating this annex, but now it's looking good on my server:

root@titan.local:/tank/Media/Pictures# git annex status
supported backends: SHA256E SHA1E SHA512E SHA224E SHA384E SHA256 SHA1 SHA512 SHA224 SHA384 WORM URL
supported remote types: git S3 bup directory rsync web hook
trusted repositories: 0
semitrusted repositories: 2
        00000000-0000-0000-0000-000000000001 -- web
        be88bc5a-17e2-11e2-a99b-d388d4437350 -- here (titan)
untrusted repositories: 0
dead repositories: 5
        0A9F3136-A12A-43C7-9BE2-33F59954FD52 -- vulcan
        57349F02-E497-4420-9230-6B15D8AB14EE -- vulcan
        6195C912-2707-4B75-AC8C-11C51FAA8FE0 -- vulcan
        D51DEDC4-9255-4A99-8520-2B1CED337674 -- hermes
        EE327B34-3E20-4B5B-8F0E-D500CBC9738D -- hermes
transfers in progress: none
available local disk space: unknown
local annex keys: 20064
local annex size: 217 gigabytes
known annex keys: 21496
known annex size: 217 gigabytes
bloom filter size: 16 mebibytes (4% full)
backend usage: 
        SHA256E: 41560
root@titan.local:/tank/Media/Pictures# git annex unused
unused . (checking for unused data...) ok

It passes git annex fsck without any problems. However, when I "git clone" this annex to my desktop machine and then do a git annex sync, I see this:

Vulcan /Volumes/tank/Media/Pictures (master) $ git annex status
supported backends: SHA256E SHA1E SHA512E SHA224E SHA384E SHA256 SHA1 SHA512 SHA224 SHA384 WORM URL
supported remote types: git S3 bup directory rsync web hook
trusted repositories: 0
semitrusted repositories: 5
        00000000-0000-0000-0000-000000000001 -- web
        0A9F3136-A12A-43C7-9BE2-33F59954FD52 -- vulcan
        274D3474-7A25-44CD-8368-CF11C451014F -- here (vulcan)
        EE327B34-3E20-4B5B-8F0E-D500CBC9738D -- hermes
        be88bc5a-17e2-11e2-a99b-d388d4437350 -- titan
untrusted repositories: 0
dead repositories: 3
        57349F02-E497-4420-9230-6B15D8AB14EE -- vulcan
        6195C912-2707-4B75-AC8C-11C51FAA8FE0 -- vulcan
        D51DEDC4-9255-4A99-8520-2B1CED337674 -- hermes
transfers in progress: none
available local disk space: 1 terabyte (+1 megabyte reserved)
local annex keys: 0
local annex size: 0 bytes
known annex keys: 21025
known annex size: 217 gigabytes
bloom filter size: 16 mebibytes (0% full)
backend usage: 
        SHA256: 18707
        SHA256E: 2318

Where did all these SHA256 keys come from?

Why doesn't the known annex keys size match?

Further, I cannot git annex get on most of the files, because it says that the SHA256 key is not present.

It looks like I'll have to rollback my ZFS snapshots and start over, but I'm wondering: how was I even able to create this situation?

Done; user error. --Joey