For anyone else reading along, I opened a bug for this issue here:
https://bugzilla.ipfire.org/show_bug.cgi?id=13736
Adolf is working on a patch. I will wait for the patch to be released, upgrade to whichever CU it happens to be in, make a fresh backup (which should now not include makeqosscripts.pl), then do a fresh install and restore, which should then get me current with QoS and CAKE.
Thanks for all your help, Adolf.