After trying focusing manual during video record with help of chdk sx220hs-101.a-1.0.0-1699 full beta and same named camera I notice wat autofocus became noisy, click-like.
Does it do this with CHDK disabled (unlock the card if you are using autoboot).
Are you certain this isn't due to some other setting changed ? For example, aperture changes or putting the ND in or out can make clicks. These depend on camera settings and lighting. It's also worth noting that these cameras do tend to get noisier with use, although I wouldn't expect sudden changes.
It is a problem then I record video, I hear "cliks" of autofocus. Is this permanent? Wat can I do to fix it?
It's highly unlikely that CHDK changed what the hardware does if CHDK is not running. If it has in fact happened, then chances are no one can tell you how to fix it, because we've never experienced it before.