System Workbench for STM32

Yes, I had forgotten about that. The 'step by step' procedure (I cannot take credit for that) does have you rename the project and folder which would cause problems regenerating sources using MX.

I suppose you could undo the renaming steps, run MX and then redo the renaming steps. That's a little cumbersome. The other alternative would be to regenerate the folders in another location and copy the changes and/or changed files to your working project. Again, you could use something like git to identify the changes.