The Unknown has a non-agression pact with The Dysonians. Trying to attack a Dysonian brought up the message asking if i wanted to break the pact (i'm an officer if that makes any difference), so i clicked cancel... but the dysonian remains on my tab.. they weren't bumped...

You need to click the Battle tab to refresh after opening a NAP'd or truced/halc'd ship.

I just checked and it worked fine for me.

I was under the impression that the enemy would be taken off your BT automatically if you tried to hit them. If it doesn't, then it really should. It's not obvious that you need to reload the BT. The game updates automatically with other actions, such as using a planet purger, so I don't see why this is different.