Now it starts to make sense, let's see if the following definitely clears the issue.
A .iso is a CD and a CD is a .iso.
They are PERFECTLY the same thing, the difference being only that THE SAME EXACT data in one case is saved inside a file on your hard disk and in the other case it is saved on an optical media.
A "full" cycle is:
Source(CD or .iso)->access Source->copy (or if you prefer extract) contents
to HD->modify copy of contents
->create Target ( .iso) ->burn Target to CD
What you need as Source is NOT the CD, nor the .iso, but the contents
of either of them.
In the case of .iso, you can open it with FREEWARE 7-zip:http://www.7-zip.org/
allright (in order to copy it's contents to HD) or you can use ANY of the several "Virtual Disk Drivers" available to MOUNT the .iso wxactly as if it was a CD (in order to copy it's contents to HD).
The most prominent FREEWARE ones are (in no apparent order):
Virtual Clone Drive:http://www.slysoft.com/en/virtual-clonedrive.html
but there are many more.
And most support command line, so that you can automate the procedure via Batch or whatever.
Once you have modified the copy of the Source and created the .iso, in your described scenario there is NOT one need in the world to "burn" it (if not to test the result on real hardware).