First, I'd just like to clarify that the chereme is not “the emic unit” for signed languages, but rather the signed version of a phoneme — which indeed is exactly the cause for what you noticed. Due to the exact parallel between chereology and phonology, linguists have generally agreed to simply use the same terms as in spoken languages.
One way of understanding this decision is to consider the other emic units of signed language: just because the mode and medium have changed doesn't mean we use different words for the syntax, pragmatics, and semantics of signed languages. Phonology is completely parallel in spoken and signed languages, so there's arguably no reason to differentiate between them.
You also asked “by what discourse communities” has this terminology been abandoned. If you meant “whose decision was it,” I'm not sure (though I would guess linguists at large), but if you meant “who no longer uses this terminology,” I can say that phonology/phonemes is what both my Deaf ASL professor and my linguistics professors use.
(And, just to add a third-party source, I also found this passage from 2006 in the Encyclopedia of Language & Linguistics, in the section on William Stokoe:)
…Stokoe's cheremic terminology has been discarded (it is now usual for sign language linguists to refer to the phonology of signed languages)…