I just dowloaded the 1.4.1 version and I can confirm the problem is gone. And to be safe, I also undid the changes I did in the ".project" file. Thanks for the quick fix.

Thanks for the info. I tried creating a new project and change back the:<nature>com.st.stm32cube.ide.mcu.MCUCubeIdeServicesRevAev2ProjectNature</nature>to the one giving me problems:<nature>com.st.stm32cube.ide.mcu.MCUCubeIdeServicesRevAProjectNature...

@Cartu38 OpenDev​ Maybe projects created on the latests versions of STM32CubeIDE don't have this problem. I started working on this project since STM32CubeIDE 1.0.2.

After comparing the new project created using the .ioc file (the one that doesn't have this problem) with my project (that have this problem) I've seen that this line in the ".project" file is the one making the difference:This line gives the problem...

Thank you very much for your help. If I create a new project using the .ioc file, it compiles fine and it doesn't gets deleted when the code is generated from CubeMX. So it has to be something related to the project.