I might have resolved the problem, I removed all the files which were in "HardDisc4" in Virtual Store after I had copies them to the correct location in the "real" "HardDisc4" within the Virtual Acorn program file.
I then did a right click over the folder "Virtual Acorn RiscPC" in the Virtual Store and "took Ownership of all the files stored there" and deleted them, so far the files which I have copied from my real RiscPC to VA have not re-appeared in the wrong place.
If, as I believe this is the answer, then the above may be of interest to other VA users. I also think that the other issues which I posted on the forum re VA since installing Windows 8.1 were caused by files which I did not know were still on my PC getting in the way of a clean installation of VA.
I have also taken ownership of all the files on the HardDisc4 in the VA program file, I hope my problems are solved!!