Hi Lukas,
We tried your suggestions.
1. Uninstall the MCUXpresso IDE 11.1.1
2. Remove c:\ProgramData\NXP\mcu_data_v8\ directory
3. Install the MCUXpresso IDE 11.2.0
and update sdk but result not changed. Not sure what you mean by " each time we opened your project the missing parts were added." When we tried to open project with another windows10 or linux machine, there is no warning or no error.