Ive sent in the camera + lens twice. Once when the lens and body had separate issues and they seemed to have been calibrated together and once because I specifically wanted a lens to be calibrated to my 5d. Based on those and my other experiences with CPS, I would guess that readjusting a lens to a camera probably does affect AF on other lenses, but may or may not be visually apparent.
If you are having a front/back focusing issue, what you want is MFA, so you can manually adjust the front/back focusing of an individual lens. A feature not in the 60d, but is found in various upgrades. If your body is under warranty, I would consider sending both lenses with the body with as much information and examples, with EXIF information, of your focusing issue that you can provide and hope that they find some happy medium.
Another potential issue is decentering from impact. This would appear as portions of your image always out of focus while other portions remain in focus or the focusing just doesnt seem to make sense when you look at the image. If this is your problem and you are out of warranty, the cost of repair becomes an issue, i.e. cheaper to buy a replacement 18-55 then repair it. If it a mechanical lens issue and you are somewhat handy, you might be able to reapir the lens itself. Look for a video with your issue and someone can guide you step by stpe.
good luck