Robert_Charlton - 6:46 pm on Nov 12, 2012 (gmt 0)
I was actually thinking of just shelving the affected brand.net and starting afresh with the brand.co.uk not redirecting anything to brand.co.uk.
Does "afresh" include new content? If so, I believe that what I said previously and am requoting below would apply... though I should add that I've not done this....
I believe that the move should work in the case of Penguin, assuming that...
a) all your problems were link-related (with no spammy onsite techniques)...
b) there had been no additional promotion of brand.co.uk (ie, links built to it and redirected to the .net).
c) the new links you build are not artificial.
If the content is the same or substantially similar, I don't know whether it would be considered duplicate. Google currently seems to be working on the basis of the highest authority wins.
If you're planning to keep current content, then you might want to consider disavowal on the .net first, assuming that it has some really good links (ie, freely given editorial links from good, relevant sites) worth preserving. In this case, I think I'd try keeping those and doing a massive disavowal on the .net for the rest. You'd have to give it some time, though, as disavowal of the old links could take a while to unwind.
PS: You could also try this disavowal on the .net while building a new, unconnected site on the .co.uk. It would be best for the content to be very different.