From my experience using other IDEs like SW4STM32, it is best to open CubeMX do your design and then select your IDE through MX. I have been working with many combo weirdness when it comes to which IDE and MX to use. There are other tools like STM STudio which has shown some non-functional operation with STMCubeIDE. Also you must note how the tools manage their workplaces. Keep in mind there might be times when you want to go-back to MX from your IDE space to make a change and have this change reflected back into the IDE space with your old code still in tact. I found this to be a problem as well if not careful.
Here is another weird thing you want to watch for. Since I was going back and forth between SW4STM32 and STM32CubeIDE, I noted the last IDE tool used left remnants of its use in the MX install environment. I'm sure some environment variable is left in the background - who knows where. So, if I would select CubeIDE after using SW4STM32, the MX tool would not open the newly selected IDE tool. What I had to do is close MX, then open the newly selected IDE, as stand alone, not from within CubeMX, and it would come up and say "the .cproject and project" has been associated with another IDE tool - "would you like to switch the association?" I would answer yes and then go back through CubeMX and the newly selected IDE would open as instructed inside CubeMX.
What I suggest, and have done for myself is to start working with STMCubeMX and STMCubeIDE as a combo. The new CubeIDE also has "Live Expression" which takes the place of ST Studio as far as I'm concerned. I found the tools to respect each others space and seem to work better together.
