I already broke it.
The first thing I noticed.
Node Project and NodeJS version manager puts node+npm+yarn+pm2 in the folder www/server/nodejs apparently only for itself because globally node is not installed in the fresh installation.
So either I or in place of pm2 module installs nvm also with node+npm+yarn+pm2 but globally.
When I installed NodeProject I installed version 16.15.1 and so until I brought it up to 16.16.0 it just didn't want to work.
But that's not the point.
The point is that my software is responsible for installing the application and installing packages. It does copy and call globally installed "npm install" itself when it's first run and also updates all the applications when needed, and when I after installing an application in Node Manajer it tries to update the whole thing because it uses yarn which I don't work with. Yarn starts doing magic and after that I get either an access error or failed to activate. In order to fix it I have to either click on project folder and restore permissions or reinstall node_modules completely.
I've noticed before that yarn is not friendly with npm in the same project
Yes, there is also a difference in permissions.
Since my program creates applications as root and these same permissions are transferred to folders in Project Manager with the setting on the www begins to have problems.
Thank you for your help