Unexpected output in Batch replace all

A list of replacements was used on the file source-text.txt: File content:

*(/afaistos
*(/agios
*(/agnwn
*(/alh
*(/alios
*(/alis
*(/almos
*(/alukos
*(/alus
*(/arma

In Notepad++ as notepadplusplus-findreplace.txt Then the Python script Plugin was used to batch replace the characters The script:

with open('C:/notepadplusplus-findreplace.txt') as f:
    for l in f:
        s = l.split()
        editor.replace(s[0], s[1])

The output was as expected (notepad-output.txt):

Ἅφαιστοσ
Ἅγιοσ
Ἅγνων
Ἅλη
Ἅλιοσ
Ἅλισ
Ἅλμοσ
Ἅλυκοσ
Ἅλυσ
Ἅρμα

Tried same replacements with EmEditor with batch replace (emeditor-findreplace.tsv). The output was unexpected, i.e.

Ἅφὰὶστὸσ
Ἅγὶὸσ
Ἅγνὼν
Ἅλὴ
Ἅλὶὸσ
Ἅλὶσ
Ἅλμὸσ
Ἅλὺκὸσ
Ἅλὺσ
Ἅρμὰ

Any ideas why this difference? I suspect that replacements might not be done in a linear fashion which is important for this type of conversion. Files here