assuming that you know roughly what you are doing I don't see why you couldn't stop it, copy the files to a new location, edit the F@H section of the registr and edit the folding service to point to the new locations.
Of course editing the registry can kill your machine stone dead so be careful in there
I just run -configonly and tell it not to run as a service, then move it, run -configonly again and set it to run as a service again, then go into the registry and put the flags back in (-local -verbosity 9 -forceasm) and then start the service(s).
This is offtopic but SS, your sig is oversize. If you're using an image you are allowed but one line of text in accompaniment. I'm just trying to keep you from the ignominious yellow sig.
EDIT: Also, I think you mean to say you like the dark brown color at "EOC" rather than "ECO".
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