I think a large part of the decision in CS (although I may be misremembering) was because the custodial sentence was replaced by a hospital order, so it took effect as if the hospital order was originally imposed when the custodial sentence was. I recall a point being that the patient would be disadvantaged if they were unable to pursue their application because they were successful in their appeal to the CrCoA.
There’s a clear semantic difference between:
a) P applying whilst on a s.47/49 or s.48/49, but then being sentenced to a s.37/41 (judicial oversight of the crown court breaking the chain); and
b) P applying whilst on a s.47/49, but their custodial sentence being retroactively replaced by the Court of Appeal (no judicial oversight about whether the patient should presently be under s.37/41).
Recognising I’m perhaps commenting on what I think the law should be than what it is, but in my eyes judicial oversight appears determinative (if we ignore AC).