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Give it a try... can't hurt anything.
Keep in mind that there are apps that can't work properly with all of their files in \Windows. Some apps need to see some files in specific places (or subfolders from where the main files are) so make sure you use initflashfiles to copy any such files to where they need to be.
That method is still going to grab the uninstall info. But as you don't try to uninstall anything then that may not be a problem. I'm not sure of any possible consequences of overwriting some of the hard-core OS registry keys but there's only one way to find out.
Please report back on your results. Good luck.
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