This morning, I wanted to restart an already existing Docker container:
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$ sudo docker start my_container
failed to update store for object type *libnetwork.endpointCnt: Key not found in store
[SOLUTION]
On my setup, the /var/lib/docker folder is a mountpoint for a larger disk - which wasn't mounted automatically, so Docker saw an "old", underlying installation structure. Therefore it couldn't find its keys...
But "mount --bind ..." didn't help, because Docker needs to restart to load its stuff properly.
Anyways:
Make sure your /var/lib/docker is as sane as your setup requires it, then restart docker:
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$ sudo systemctl restart docker