Hi,
actually you only need custom debugger scripts for that.
We usually use Lauterbach debugger which offer scripting and its quite easy to load multiple output files in one program cycle.
lauterbach reads the flash content, then modify it ( no matter how many operation you do), and load the modified content back to flash.
In this way you don't need to merge output files and you can achieve what you are looking for.
I expect that most of flash/debug tools uses same strategy.
If you are not sure how to do it I suggest you to contact you debug vendor.
Peter
