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The Gemara Berachos (32b) says
אָמַר רַבִּי יוֹחָנָן: כׇּל כֹּהֵן שֶׁהָרַג אֶת הַנֶּפֶשׁ — לֹא יִשָּׂא אֶת כַּפָּיו - Rabbi Yoḥanan said: Any Kohen who killed a nefesh may not lift his hands in Birkas Kohanim.
If the nefesh is a part (albeit the lowest aspect) of the infinite soul, what does it mean to "kill" that part of the soul?
This is an idiom for killed a human being. As we see in various other places as well. That is why the Rambam, the gemara and other places including tanach use that term when referring to the death of a human being. Another example is the use of פיקוח נפש (pikuach nefesh) which means saving a life and not saving the soul. When an idiom is used one cannot translate the words of the idiom literally.
See Zohar brought here - http://www.aspaklaria.info/080_PE/%D7%A4%D7%A0%D7%97%D7%A1.htm
תא חזי, כל כהן שהרג נפש הוא פסול לכהונה לעולם, כי הוא פסל ודאי את המדרגה שלו אליו, (כי הכהונה היא מדרגת חסד, והריגת נפש היא הפוכו), ופנחס (כיון שהרג את זמרי וכזבי) נפסל מן הדין להיות עוד כהן, ומשום שקנא להקב"ה היה צריך לתת לו מחדש כהונת עולם לו ולזרעו אחריו לדורי דורות. א"ר יצחק תא חזי, רשום הוא פנחס למעלה ורשום הוא למטה, (למעלה היינו מטרם שבא לעולם, למטה שהרי נמנה עם אלו שיצאו ממצרים.
Come and see, every cohen who kills a soul becomes invalidated for the priesthood forever, for he certainly has invalidated his level, and Pinchas was invalidated according to the strict letter of the law, and because he was zealous for Hashem, He had to give him anew eternal priesthood for him and his descendants for all generations. Said Rabbi Yitzchak, "Come and see, Pinchas is mentioned above and he is mentioned below."
The Zohar is enigmatic. If Pinchas was invalidated from the kehunah, how did it help for Hashem to regrant him the kehuna, and why does the Zohar make repeated references to the eternity of kehunah?
I think it is the Satmar Rov (although I can't find this at the moment) who explains the Zohar as follows:
The point here of the nephesh is that the nephesh is the lowest part of the soul, which is bent down to reach olam ha'zeh. Therefore the nephesh is most important, because it is exactly at the meeting point of the soul with olam ha'zeh that we have "happening" and evolution of the human condition.
The purpose of the cohen is to ensure that the evolution of the human condition is consistent with the original intention of creation of man, which is why priesthood is a bris - covenant.
Therefore Pinchos was invalidated from being a cohen because he killed a soul. This means, since the purpose of the priesthood is to ensure that man's evolution continues according to its original intention, therefore if a cohen kills a soul, he invalidates himself from the kehunah because he has terminated that evolution (for whatever reason).
Therefore Hashem had to reconnect Pinchas to the line of human progress that begins with the initial creation of Adam and that continues with the continual chain of all generations.
It just means to kill a person, to commit murder, as the Rambam explained:
A priest who has slain a human being, even if he has repented, must not perform this rite, for it is said, "Your hands are full of blood" [Isaiah 1:15]. [Mishneh Torah, Prayer and the Priestly Blessing 15:3; Shulchan Arukh, Orach Chayim 128:35]
See Chinuch mitsvat 263, about the prohibition for cohanim to get uncleanness from a death. לנפש לא יטמא בעמיו
ואף על פי שנפש טובה לא תמות יענה הכתוב הגוף בשם הנפש כי היא העיקר
Despite that the good soul would not die, the scripture calls the body "soul" because it's the main.
