Well no, but let me explain...
Certainly setting the wrong value in the AF Adjust menu on your camera can make the AF perform worse. That would be like setting the aperture wrong will make the exposure wrong. So of course you should be careful use the precision LensAlign, and pay attention to detail when adjusting the AF Adjust. Also setting at too close a distance is not good.
BUT, like switching the camera over to auto exposure to correct for a wrongly set aperture, all DSLRs that have the AF Adjust feature allow you to disable it in 2 ways, either of which will restore the camera/lens back to its performance before the adjustment was made.
1 - You can simply turn the AF Adjust feature OFF. This will maintain all of the adjustments that you have made for your lenses, but will tell the AF system to ignore them and perform as if the adjustments were never made.
2 - You can turn a specific lens OFF, by resetting its adjustment setting to 0 (zero). of course you should write down the setting if you would like to restore it at a later time.
Bottom line...you cannot damage you camera or lens or cause permanent performance degradation by using the AF Adjust system.
If you already have an AF Adjustment setting in the camera from a previous test session, make sure to write it down, so that it can be restored (manually by you), in case the new test session is interrupted or for some reason you wish to go back to your previous setting.