It says in Shulchan Aruch, Orach Chaim Siman 110, that certain poalim (workers) must daven a normal shemoneh esrei, but they shouldn’t be “yored lifnei hateivah” or make birkas kohanim, since this would be too much and the employer would be makpid.
What is the halachah when the Kohanim are ‘called’ to duchan, so that if they don’t go they transgress a Torah mitzvah (three mitzvos)? Must they still not go to duchan because of the kepeidah of the employer?
The Gemara (Berachos 46a) writes that the berachah of ha-tov veha-meitiv is rabbinic, for were this not the case, it would not be possible to enact that workers should not recite it.
This shows that it is one must not miss out on a Torah mitzvah on account of one’s working obligations.
On the other hand, Tosafos (Berachos 16a, s.v. ve-chosem) writes that Chazal have the power to uproot even Torah mitzvos for the purpose of the employer’s rights (his being particular in this), and therefore explain how one of the three principle berachos is omitted.
However, this is difficult (as Rabbi Akiva Eiger notes) from the Gemara above, and the Magen Avraham (191:1) suggests an alternative explanation, so that the simple view remains that one may not trangress (meaning, fail to perform) a Torah mitzvah because of the consideration of poa’lim.
Concerning Birkas Ha-Kohanim, it therefore appears that the intention of the Shulchan Aruch (as based on Chazal, see Berachos loc. cit.) is that the workers leave shul after their private shemoneh esrei, so that they don’t get involved in the Torah obligation of Birkas Ha-Kohanim.
If the Kohen is still in shul and the Kohanim are called up, so that the Torah mitzvah applies, it appears that the Kohen will have to rise to the duchan, in spite of his employer’s possible kepeidah.
Note that the Shulchan Aruch writes that today, these halachos don’t generally apply, because employers are not as particular as they once were. However, this refers to general workers who “work all day,” and application to each person will depend on the personal contract with his employer.