You have to dismiss it and after you are through changing the setup set it as escort again.

The answer to your question is yes, you can.

An escort ship is simply a DD or CL class ship to which you already own, and have crew to run. This crew, would of course be in exclusion to the ones that you would be actually playing with at the time. To modify the ship, you would just need to modify the ship just as though you normally would. Once you have the setup like you wish, then you would use the escort settings tool to form the escort. To change the setup, you would then just dismiss the escort, and make any modifications that you needed and reform. 

Thanks,
Poage
TeamNF - Kaiser 

i hit dismiss and it disappeared along with the crew.

nvm found it thnx guys.

My escort regularly self dismisses. It happen about once every ten times I use it.  This costs money to reform it each time.

Is this a recognised bug?