Looking at the schematics I see the following:
Shorting J17 is used to manually turn power on or off to the ESC's. Having J17 shorted will not hurt anything, it just means that power will be applied all the time to the ESC's.
Shorting J12 is the manual switch to turn power off and on to the ROV if you do not have +5v on the tether to do this for you. Having this jumper installed will not hurt anything, it just keeps the power turned on all the time to the ROV.
I will let Walt or others answer this question about J7 as I do not have the 2.5V cape yet to play with. I would not jumper this as it looks like it may be used to apply voltage to the Servo rather than short to ground. Shorting to ground with the esc's connected may cause issues.
This jumper on the old cape was used to apply +5V to the Servo motor on the web cam if you did not have any ESC's connected. If you had ESC's connected then the jumper would be removed and the esc's would supply the +5V needed for the servo.