Look like the STM32 board configuration in your project has not been applied (missing compiler prefix, core options, symbols...).
Did you select “Retore Default” in the project properties page ? It could explain why many build options has been erased.
I think the easiest way to resolve this problem is to create a new project. If the issue is persistant, contact us again, we will make further investigation (tell us board and the firmware you’ve chosen).