plugins’ settings will be cleared when notepad++ restarting

Plugins are responsible for tracking their own settings, not Notepad++.

Usually plugins keep track of their settings using config files in one of the following:

• %AppData%\Notepad++\plugins\config (if the Notepad++ executable is in ProgramFiles)
• for portable installations, nppDir\plugins\Config, where nppDir is the root directory of the portable installation (I think this is what you have)

I suspect that the plugins couldn’t find the directory where they would normally save the config files, or else that they saved the config files in the wrong location. Maybe one of those plugin authors forgot to consider portable installations when they were deciding how to save their settings.