I also have a similar problem, generated project through CubeMX but unable to flash or debug. For me it worked editing the .cproject file.
All i needed to do was to change any entries of fr.ac6.managedbuild.option.gnu.cross.board, from 32F769IDISCOVERY to STM32F769I-DISCO.
Of course you have to modify yours accordingly.
Hope this might help someone as I really lost quite long time finding what the issue was.