Sometimes the user manual may be unclear and you came here searching for a solution of dropping a published repository.
We have aptly version: 1.3.0 and here is the right syntax to remove a published repository.

First list the published repositories and reverse the “/” replacing it with space

The commands will be:

aptly publish list
Published repositories:
  * <name-distribution>/<release> [amd64] publishes {main: [xenial-<name>]: Some description}
aptly publish drop -force-drop <release> <name-distribution>

“name-distribution” is the “http://aptly.example.com/[name-distribution]” in the URL. For example, the repository URL of myrepo is “http://aptly.example.com/myrepo” and the name-distribution is “myrepo”.

A real world example

root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish list
Published repositories:
  * myrepo/stable [amd64] publishes {main: [xenial-myrepo]: Stable myrepo packages}
  * test/test [amd64] publishes {test: [test]: Test repo}
root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish list --raw
myrepo stable
test test

We want to remove “myrepo/stable”:

root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish drop -force-drop stable myrepo
Removing /etc/aptly/.aptly/public/etc/dists...
Removing /etc/aptly/.aptly/public/etc/pool...

The published repository has been removed successfully.
root@srv-aptly:~#

The wrong syntax

You might have tried it that’s why you came here:

root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish list           
Published repositories:
  * myrepo/stable [amd64] publishes {main: [xenial-myrepo]: Stable myrepo packages}
  * test/test [amd64] publishes {test: [test]: Test repo}
root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish list --raw
myrepo stable
test test
root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish drop myrepo
ERROR: unable to remove: published repo with storage:prefix/distribution ./myrepo not found
root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish drop myrepo stable
ERROR: unable to remove: published repo with storage:prefix/distribution stable/myrepo not found
root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish drop myrepo-stable
ERROR: unable to remove: published repo with storage:prefix/distribution ./myrepo-stable not found
root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish drop -force-drop myrepo-stable
ERROR: unable to remove: published repo with storage:prefix/distribution ./myrepo-stable not found
root@srv-aptly:~# aptly --config="/etc/aptly/.aptly.conf" publish drop -force-drop myrepo stable
ERROR: unable to remove: published repo with storage:prefix/distribution stable/myrepo not found
root@srv-aptly:~#