Adriane's description of the issue is spot on. There is also another consideration to keep in mind with qui and quis, in that qui quis also have the peculiarity that the Romans did not like the sound of an s too close after quis, so often shortened it to qui, and the other way around as well, increasing qui to quis, if followed by a vowel. So, the Romans played fast and loose with the substantive/relative interrogatives.
So, there is no way of knowing if qui discipulus is not actually quis discipulus. The number of s sounds in discipulus might perhaps have displeased a Roman ear, leading to the s on quis being dropped off. It certainly sounds less hissy to say qui discipulus, than quis discipulus.
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