Please describe the problem.

I've added a backup USB Drive and a small archive USB drive and created a archive folder in the root of my ~/annex folder.

If I move a file into the ~/annex folder and then move the same file into the ~/annex/archive folder the file gets uploaded to the small archive USB drive, but not dropped from my ~/annex/archive folder.

[2015-08-14 19:03:47 CEST] Committer: Adding git-annex..iving.ogv
ok
(recording state in git...)
(recording state in git...)
(recording state in git...)
add /Users/markus/annex/git-annex-assistant-archiving.ogv [2015-08-14 19:03:47 CEST] Committer: Committing changes to git
[2015-08-14 19:03:47 CEST] Pusher: Syncing with annexbackup, annexarchive

git-annex-assistant-archiving.ogv
To /Volumes/annex-archive/annex-archive0
   6ef9226..6c87a7d  git-annex -> synced/git-annex
   b8855cc..bc20ee2  annex/direct/master -> synced/master
To /Volumes/annex-backup/annex-backup
   6ef9226..6c87a7d  git-annex -> synced/git-annex
   b8855cc..bc20ee2  annex/direct/master -> synced/master
    15428954 100%   20.71MB/s    0:00:00 (xfer#1, to-check=0/1)

sent 15430948 bytes  received 42 bytes  10287326.67 bytes/sec
total size is 15428954  speedup is 1.00
[2015-08-14 19:03:48 CEST] Transferrer: Uploaded git-annex..iving.ogv
[2015-08-14 19:03:49 CEST] Pusher: Syncing with annexbackup, annexarchive
To /Volumes/annex-backup/annex-backup
   6c87a7d..d24edd5  git-annex -> synced/git-annex
To /Volumes/annex-archive/annex-archive
   6c87a7d..d24edd5  git-annex -> synced/git-annex
[2015-08-14 19:04:23 CEST] Committer: Adding git-annex..iving.ogv
ok
(recording state in git...)
(recording state in git...)
(recording state in git...)
add /Users/markus/annex/archive/git-annex-assistant-archiving.ogv [2015-08-14 19:04:23 CEST] Committer: Committing changes to git
[2015-08-14 19:04:23 CEST] Pusher: Syncing with annexbackup, annexarchive

git-annex-assistant-archiving.ogv
To /Volumes/annex-backup/annex-backup:00
   d24edd5..507be0c  git-annex -> synced/git-annex
   bc20ee2..8fea81a  annex/direct/master -> synced/master
To /Volumes/annex-archive/annex-archive
   d24edd5..507be0c  git-annex -> synced/git-annex
   bc20ee2..8fea81a  annex/direct/master -> synced/master
    15428954 100%   30.72MB/s    0:00:00 (xfer#1, to-check=0/1)

sent 15430948 bytes  received 42 bytes  30861980.00 bytes/sec
total size is 15428954  speedup is 1.00
[2015-08-14 19:04:23 CEST] Transferrer: Uploaded git-annex..iving.ogv
[2015-08-14 19:04:25 CEST] Pusher: Syncing with annexbackup, annexarchive
To /Volumes/annex-archive/annex-archive
   507be0c..ba58f77  git-annex -> synced/git-annex
To /Volumes/annex-backup/annex-backup
   507be0c..ba58f77  git-annex -> synced/git-annex

If I directly move a file e.g. from ~/Downloads to ~/annex/archive the file gets uploaded to the small archive USB drive and then dropped from my drive (as expected).

[2015-08-14 19:04:25 CEST] Pusher: Syncing with annexbackup, annexarchive
To /Volumes/annex-archive/annex-archive
   507be0c..ba58f77  git-annex -> synced/git-annex
To /Volumes/annex-backup/annex-backup
   507be0c..ba58f77  git-annex -> synced/git-annex
[2015-08-14 19:09:44 CEST] Committer: Adding Oracle_VM..x-extpack
ok
(recording state in git...)
(recording state in git...)
(recording state in git...)
add /Users/markus/annex/archive/Oracle_VM_VirtualBox_Extension_Pack-5.0.0-101573.vbox-extpack [2015-08-14 19:09:44 CEST] Committer: Committing changes to git
[2015-08-14 19:09:44 CEST] Pusher: Syncing with annexbackup, annexarchive

Oracle_VM_VirtualBox_Extension_Pack-5.0.0-101573.vbox-extpack
To /Volumes/annex-backup/annex-backup:00
   ba58f77..73eed9e  git-annex -> synced/git-annex
   8fea81a..68526f7  annex/direct/master -> synced/master
To /Volumes/annex-archive/annex-archive
   ba58f77..73eed9e  git-annex -> synced/git-annex
   8fea81a..68526f7  annex/direct/master -> synced/master
    18028050 100%   25.65MB/s    0:00:00 (xfer#1, to-check=0/1)

sent 18030392 bytes  received 42 bytes  12020289.33 bytes/sec
total size is 18028050  speedup is 1.00
[2015-08-14 19:09:45 CEST] Transferrer: Uploaded Oracle_VM..x-extpack
ok
(recording state in git...)
(recording state in git...)
drop /Users/markus/annex/archive/Oracle_VM_VirtualBox_Extension_Pack-5.0.0-101573.vbox-extpack [2015-08-14 19:09:47 CEST] Pusher: Syncing with annexbackup, annexarchive
To /Volumes/annex-backup/annex-backup
   73eed9e..93dc4a3  git-annex -> synced/git-annex
To /Volumes/annex-archive/annex-archive
   73eed9e..93dc4a3  git-annex -> synced/git-annex

But if I move the file-link from ~/annex/archive to ~/annex the file stays a link and don't get transferred back to my drive.

[2015-08-14 19:12:39 CEST] Committer: Committing changes to git
[2015-08-14 19:12:39 CEST] Pusher: Syncing with annexbackup, annexarchive
To /Volumes/annex-backup/annex-backup
   68526f7..082e0d8  annex/direct/master -> synced/master
To /Volumes/annex-archive/annex-archive
   68526f7..082e0d8  annex/direct/master -> synced/master

What version of git-annex are you using? On what operating system?

Im using MacOSX 10.11 Beta (15A243d) with the most resend MacOSX App.

$ /Applications/git-annex.app/Contents/MacOS/git-annex version
git-annex version: 5.20150812-ga6f7b36
build flags: Assistant Webapp Webapp-secure Pairing Testsuite S3 WebDAV FsEvents XMPP DNS Feeds Quvi TDFA TorrentParser Database
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt S3 bup directory rsync web bittorrent webdav tahoe glacier ddar hook external
local repository version: 5
supported repository version: 5
upgrade supported from repository versions: 0 1 2 4