This is basically attested from Albanian: word-initial *sp *st *sk > /f ʃt h/. Some sources suggest that there was an intermediate step with metathesis to *ps *ks, another route could be debuccalization or aspiration spreading through *spʰ *stʰ *skʰ. (Compare Middle Indic: /sp st sc sk/ > initial /pʰ tʰ cʰ kʰ/, medial /ppʰ ttʰ ccʰ kkʰ/.)
Also, digging up some older questions:
Closest I know of is Mator, where *Vjt > Vst, entirely possibly through *Vʃt (just this one cluster though; no change in *Vjʔ at least).
Kodagu has both [ɨ ɯ], but they don't contrast. [ɨ] is an epenthetic unstressed vowel and only /ɯ/ is phonemic.
As far as phonological representation goes, in principle /ɨ ɯ/ can be still both represented with just [±front ±labial], via underspecification: one of them as [-front] (or [+back]) with no labiality specified, the other as [-labial] with no frontness specified.
A third simple possibility is that in several languages, what gets called "/ɨ/" is phonologically [-high] (or at least not specified as [+high]) and could be also described as /ə/ with a relatively high realization.