The deleting has nothing to do with the "User Already Logged In" issue. This is caused when an account get locked into the server so it thinks that the account is already online. Like said above, you'll have to wait for a reboot, which usually happens at least once per day.
In the future, make sure that you're hitting log out from the escape menu and then quitting PRO with the quit button. Don't Alt-F4 as that may increase the chances of leaving your account logged in.
As for the Pokemon releasing, you need to wait 1-2 seconds between each deleting or they don't work. It will say so in the chat window.