No genetic flaw wouldn't really take long to get rid of. A year, if everyone just stopped breeding HYPP carriers. Same with CA in Arabians.
The thing is - do you risk losing that bloodline and the potential of the great carriers (Let's say Impressive and *Ecaho) to the breeding gene pool for the sake of totally eradicating that dysfunctional gene, or do we practice good breeding practice by breeding proven carriers to non-carriers?
In the case of HYPP, I can only feel like we shouldn't even breed carriers because they can be affected fairly severely. With SCID, CA, they are double recessives and need 2 carriers to produce an affected foal. So, where, when, how do we draw the line and make sure we're correct?