Hi Chris,
Personally, if I were targeting the UK, I would use the .co.uk. I have several sites that rank pretty well in the SERPS that I target the UK for and use .co.uk domains.
I also have a uk.com site that ranks no2 for my key search term on google.com yet is 87 on .co.uk!!I bought the domain as the .co.uk was taken and switched google's webmaster geo targeting tool when the site went live and still it languishes down at a lowly 87!!!
I don't know if I am qualified enough to suggest an answer to your indexing issue and hopefully someone with more knowledge will jump in here but, you could 301 redirect your indexed pages to your new pages in .co.uk. That way google will see the change and update your site.
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