Patur- good chap about sfeik sefeika being a mesakein.
sbeth-
Alright I hear what you are saying. The way i understood rav chaim is that any mitzvah that you are vadai chayav in than safek deoraysa will not be said unless after doing it you vadai will not be chayav. therefore my case ( actually not my case i FOUND IT BY RAV MOSHE SHTernbuch who brings it as a ??raya??? farkert) in Rosh hashana is shver being that you are chayav to do a safek in the chance you are being mekayeim a mitzvah.
But you are right. If the vort is because the torah is not mechayeiv safek deoraysa which you will not know if you will be mekayeim the case from rosh hashana is not a raya.
But this is all needless as you pointed out we clearly do not pasken like this.