Flash programmer does not support that.
You can try writing a script using some softwares like Autohotkey/AutoIT..., to automate FLASH PROGRAMMER
We had written our own program for FLash programming...
We had a small EXE which used to convert S-record file contents into a C-Array.
We combined it with a .bat application to place the converted array into a file of our source code(flash burning software). We used to RUN this code to get the FLash programmed.
I guess this ws faster than the FLASH PROGRAMMER.
But when you want to DEBUG, this will be additional overhead...