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cgreen Do you still own the old domain. If you do I would use 301 redirects from the pages on the old domain to the new one. It's telling search engines 'hey these pages are now over there instead of here' and the other 50% of the links will in time be seen as pointing to the new domain.
Either way it can take a few months for the search engines to sort everything out.
One thing to know is that Google never shows all the backlinks it knows about for any site. They only show a sample of those links. So just because they aren't showing when you search in Google it doesn't mean Google hasn't found them yet.
If the people you emailed did change the links to the new domain then simply trust that Google will find them and count them as links pointing to your new domain. Google may not tell you they found them, but they will find them.
It's best to keep working at getting new links pointing to the domain and as hard as it can be not worry about Google does and doesn't know. It can take a few months for them to find all the changed links, but they will find them.
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