You don't get points for funds, they're only relevant if you're going to be invited under FSW and you are not already in Canada. The ITA letter says that you should consider rejecting the ITA if your circumstances have changed and your points have reduced - this is not the case here - they will not reduce if you remove your funds. It's your call of course but I am comfortable changing my funds to 0 - if they want proof that I have the figure I originally put down, I can provide it.
It think it's just another of the (many) flaws in the new automated system, they shouldn't even be requesting proof of funds for CEC applicants but the system is automatically generating it on the checklist because we put a figure down