First, we should figure out why that is failing.

Do:

vagrant ssh
/usr/bin/mysql -uroot -pvagrant -qfsAe "USE wikishared; SOURCE /vagrant/mediawiki/extensions/Echo/db_patches/echo_unread_wikis.sql;"

Maybe you have an old version of Echo without that file (just need to do vagrant git-update or git pull in the Echo directory).

The reason it's still running if you disabled Echo is probably that you are still using something depending on Echo.

vagrant roles list --enabled

shows what roles you have.

git grep include.*echo

shows what uses Echo.

Sorry, I posted the wrong command at first. See edited one.

I got the actual version of echo, (created that cluster temporary today, just for one experiment, and I deleted it two hours ago, but I can try to replicate it in the next days)