The notion of "sound change notation" is a bit of a problem. It is a (not unreasonable) attempt to use a device of a different domain of linguistics, but you have identified a case where the concepts of historical linguistics do not translate into the phonological analogs that you are asking about.
There is some relationship between a given synchronic phonological rule of a language, where a rule e.g. k → č /__ i in the phonology of some language is related to some series of historical changes that we might notate as k > č / __ i. In that case, you're just replacing → with > in the informal notation of a phonological rule. There is a notation for "except when" in phonology, so you could adopt that notation in your rule. It is known as the "complement notation", and is typically indicated by prefixing the symbol "~" to the relevant expression, thus e,o > i,u /__~#.