I learned from this question about sequundus > secundus that -quus was in fact pronounced as if it was -cus. However, words like equus were not spelled as ecus, since most oblique cases would still have the original stem equ- since qu>c only occurred before a u. That is, equus was pronounced ecus but was spelled equus by analogy.
I would assume that at some point the spelling equus caused the pronunciation to become equus instead of ecus again. At least this is the case in the contemporary Finnish pronunciation. I have no idea when this change happened, other than "somewhere between imperial Rome and present day Finland", but I suspect this equus pronunciation (as opposed to ecus) was not unusual in some form of medieval or later Latin. Do we know when — if ever — this change took place? When was equus pronounced as equus and no longer ecus? Any examples or a terminus ante/post quem are most welcome; I don't expect anyone to be able to point a precise point in time.