The halacha upon which your question is based – that we call “Kohanim” before Birkat Kohanim only when there are multiple kohanim – is derived by the gemara[2] from the words of the pasuk in the context of Birkat Kohanim: “Say to them”[3] (plural).[4] Several Acharonim discuss whether this applies even to your case, when there are two kohanim but only one of them is a gadol.[5]
We must first examine a katan’s status with regard to Birkat Kohanim. A mishna[6] states that a katan does not perform Birkat Kohanim, but a gemara[7] implies that a katan does perform Birkat Kohanim from the time that he knows how to do so. The Shulchan Aruch[8] reconciles the contradiction between these two sources by ruling that a katan may perform Birkat Kohanim along with gedolim in order to receive training.
The Mabit,[9] apparently the first major posek to discuss our case, rules that we do not call out “Kohanim” when the only kohanim present are one gadol along with a katan. The Mabit incorporates multiple reasons to arrive at this ruling. One of these reasons is fundamental: The Torah instructs us to prompt the kohanim regarding their obligation to do Birkat Kohanim, and a katan is not fundamentally obligated in the mitzva. Therefore, the one who calls out “Kohanim” relates only to those who are over bar mitzva. In our case, that would mean that the calling out of “Kohanim” would be for only one kohen, which is inappropriate.[10] Another point the Mabit makes is that it is a disgrace to the tzibbur to call out to the katan to bless them,[11] as doing so reflects a position of dependency.[12] He adds that there is also a problem of hefsek[13] if the chazan unnecessarily calls out Kohanim in the midst of chazarat hashatz.
Several Acharonim, including the Magen Avraham,[14] accept the Mabit’s position. However, the Pri Chadash[15] rules that we should call “Kohanim” in this situation; he is not bothered by the Mabit’s concerns. First, he argues that even if calling out “Kohanim” is our prompting of the kohanim regarding their obligation to do Birkat Kohanim, it is appropriate to include a young kohen in this prompting, since he is obligated in general to train himself in mitzvot in advance of adulthood.[16] The Pri Chadash further posits that calling out “Kohanim” is not an actual charge to bless, but rather a technical instruction to the kohanim to turn around. There is thus no declaration of dependency entailed, and calling to even a young kohen is not a disgrace to the tzibbur. Although the Pri Chadash does not address the question of hefsek explicitly, he apparently reasons that once calling is generally appropriate at this juncture of chazarat hashatz, there is no problem of hefsek.
The majority of Acharonim hold like the Mabit and do not permit calling out “Kohanim” in this situation.[17] However, several Acharonim raise a very pertinent distinction that relates to the prevalent minhag among Ashkenazim in this context. According to Sephardic custom, after concluding the beracha of Modim, the chazan recites only the word “Kohanim.” However, the Rama[18] prefers the minhag that the chazan first says the short prayer of “Elokeinu … barchenu baberacha…,” albeit differently in different scenarios. When there are no kohanim present, the entire recitation is said audibly; if there are multiple kohanim, the passage is said quietly, except for the word “Kohanim,” which is recited audibly; if there is only one kohen, the chazan recites the entire passage silently.[19] Since the same words are said in any case, calling out “Kohanim” cannot cause a problem of hefsek. Many Acharonim, including the Pri Megadim,[20] Mishna Berura,[21] and Kaf HaChayim,[22] maintain that according to this minhag, there is no problem calling out “Kohanim” for one adult and one minor kohen. The question of hefsek is even more clearly not an issue according to the prevalent minhag in Israel that someone other than the chazan calls out “Kohanim.” Interestingly, the Mabit himself does not present the matter of hefsek as the main problem in this case; apparently, since it is the only issue that can be considered an actual halachic wrongdoing, these Acharonim view it as the only claim that must be overcome in order to allow calling the kohanim. This approach may be encouraged by the fact that according to the Yerushalmi,[23] it is always proper to call out “Kohanim,” even for only one kohen.[24]
In summary, Sephardim should not call out “Kohanim” to one adult and one minor kohen.[25] Regarding Ashkenazim, if they indeed have the minhag to recite “Elokeinu …” or if it is not the chazan who calls the kohanim, either practice can be justified, and it is difficult to claim a minhag ha’olam on a relatively uncommon case.[26]