To reproduce the bug:

get some bare repo:

$ git clone --bare slapos slapos.git

backup-pull it:

$ mkdir backup && cd backup && git init
$ git-backup pull ../slapos.git/:slapos

when restoring:

$ git-backup restore HEAD slapos:../slapos.restored
$ cd .. && git clone slapos.restored slapos_bis
fatal: repository 'slapos.restored' does not exist

As @kirr explained me, it is due to git not tracking trees of empty directories:

$ls slapos.git/refs/ -Ra
slapos.git/refs/:
.  ..  heads  tags

slapos.git/refs/heads:
.  ..

slapos.git/refs/tags:
.  ..

So some directory that are used by the restored repo are missing. This is currently fixed by detecting if it is a git repo or not (it is also possible to backup usual folder/files) by verifying its extension. So it works fine when restoring this way:

$ git-backup restore HEAD slapos:../slapos.restored.git

gives:

$ cd ../slapos.restored.git && git log
commit 5f5d5102cf2dd2b4a8d092e32dfc6b87fa3bbc12
Author: [...]