As one of the authors I do agree with you that 20% EER is not the best. Since submitting this article we already went down to 10%. On gait with normal accelerometers (so not the low quality ones in the phones) we even get down to 1.5%. Still not as good as fingerprint, but on the other hand, it is unobtrusive.
If you hurt your leg permanently, then just make a new reference template. If it is just temporary, then you need to realize that this gait recognition is just an extra security measure, so you no longer need to lock your phone every time you stop using it. You principally do this because you do not want a third person to have access. With gait recognition, the phone uses the gait to recognize this third person by a different gait and will lock it then for you. A sensible implementation would unlock the phone if normal gait is detected from the correct person, but also by using a normal PIN mechanism.