If one drank a reviis [3.3 ounces] of wine or grape juice and does not know how to say al hegefen by heart, he should recite borei nefashos instead. The same applies to all foods, even bread. See Igros Moshe of HaGaon HaRav Moshe Feinstein Orach Chaim 1:74 and Kaf HaChaim 102:79.
The Mishnah Berura brings (202:42, see also 202:55 and 208:62) that if you say Borei Nefashos when you are required to make an Al HaMichya you are not yotzei even B’Dieved. You must says Boruch Shem… and then make an Al HaMichya. Even in a case where there is a Safek to say Al HaMichya or not, or if you ate something that requires Al HaMichya but did not eat the Shiur, you do not make Borei Nefashos, since these are two separate brachos that have no relationship to one another.
There are however a number of opinions that Borei Nefashos is a catch-all bracha like Shehakol. Therefore writes the Piskei Tsahuvos (208:1), although we do not pasken like these opinions even in a case of a safek, if a person does not know the Bracha Mei’ein Shalosh by heart and will lose out from making any bracha achrona, it this case he may make a Borei Nefashos and be somaich on these opinions.
Still says the Piskei Tshuvos, if he later is able to make a Bracha MaiEin Shalosh from a Siddur before digestion has ended, he should say Boruch Shem.. and then say the Bracha MeiEin Shalosh.