I find no problem to visualize Flash written blocks from running program on a MC9S08AW60 through BDM interface and USB multilink or the USB interface on the MC9S08AWDEMO board and CW5.1.
Obviously you must stop the program to navigate in the memory, but you can resume when done. Flash routine, when physically writing or erasing flash cannot be halted (or at least I didn't try).
Encoder