Mine all came either by submissions as the first site got busier, or by trawling the net looking for specific companies and discovering the email address myself (very dull, but worthwhile for the overall quality of the links I now have).

This can't be a unique problem.
Someone must have informed their Links 2.0 users that their site has changed to LinksSQL. Surely I could send an email out using something similar to the forgot password email? How would I trigger this? How do I automatically generate a password for a user who didn't need one when they used the Links 2.0 version of the site?