In version 3.0.18, add following code to user startup.py:

try:
    hello
except:
    hello = 0
hello += 1
print('hello:', hello)

Make sure that the PythonScript console window is being shown when exiting Notepad++.

Upon restarting Notepad++, the code above will show that startup.py is being executed two times:

Notepad++ Debug Info:

Notepad++ v8.6.8 (64-bit)
Build time : Jun 4 2024 - 00:30:00
Path : C:\NotepadPlusPlus\Misc_NoBackup\Releases\npp.8.6.8\npp.8.6.8.portable.x64\notepad++.exe
Command Line : -titleAdd="8.6.8 64-bit" -multiInst
Admin mode : OFF
Local Conf mode : ON
Cloud Config : OFF
Periodic Backup : ON
OS Name : Windows 11 Pro (64-bit)
OS Version : 23H2
OS Build : 22631.3593
Current ANSI codepage : 1252
Plugins :
mimeTools (3.1)
NppConverter (4.6)
NppExport (0.4)
PythonScript (3.0.18)

Probably introduced when #312 was solved.