It may affect the time it takes a clone to grow roots. It may stunt them initially a touch. Overall, if you can get it to root and grow in a healthy enviorment, the net result will be no issue. The genetics dont change from stress, if you have a killer plant and can get it healthy, it should be a killer plant again.
It may also make for a slight change in growth patterns. Maybe instead of being a sturdy plant, the clone may be stringier or even more compact if it wasnt healthy from the start, it just depends.