If the original file has a boot image, then adding files to it and saving it in another format will preserve the boot image, until and unless you tamper with the files already present on the file.
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Then, I mounted the file on a virtual drive & it ran fine.
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I was unable to understand this part. Which file did you mount? The iso or the nri?
Most probably , I have understood your overall problem. What I am telling you to do is, open the image file using MagicISO, add the files which you want to it, and then save it in ISO format instead of nrg or any other format.
MagicISO preserves all boot information and files required to boot. If it was just equivalent to copying files from an image, then it wouldn't be a separate image editing tool.
You think that if you try to add more air to an already filled and tied balloon, it will burst, and you will lose the air inside the ballon too. MagicISO helps you in such a situation. It cleverly adds more air (new data) inside the balloon, without bursting it, or even disturbing the air previously present in it

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