Can you speed up debugging in Renesas High Performance Embedded Workshop by not flashing after breakpoint
There are some options which looked likely described on Page 127 of the manual, under menu: Setup > Emulator > System. 

I changed Step over option to No programming and initially it didn't seem to help, but now it seems much faster.

It still flashes occasionally, e.g. when returning from some subroutine, but not on every line anymore - it's much better! 





I now see in the debug pane:

RUNNING
BREAK POINT
 Flash memory writing ... 
 Flash memory write end 
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
SUBROUTINE END
SUBROUTINE END
STOP ADDRESS
SUBROUTINE END
STOP ADDRESS
STOP ADDRESS
STOP ADDRESS
SUBROUTINE END


etc.