Recently when working with a SharePoint migration project from WSS 2003 site collections to WSS 2007 we ran into several undocumented limitations.
First if the content database you are trying to migrate has more than 15,000 site collections you will end up with a problem. When you run the upgrade process site collections will be missing.
Long story short the reason is that the SharePoint 2007 upgrade process generates your destination 2007 content databases for you including setting the site collection limit.
So if you have a 2003 content database with 18,000 site collections and then you run a side by side upgrade to SharePoint 2007 it will only migrate (recognize) 15,000 site collections.
How do you resolve this problem?
Well it's not easy but you will have to move site collections to a new content database in 2003. Basically rebalance so that no content database has more than 15,000 site collections. WSSSplit is a tool to help you with that task but it will take some time to run for thousands of site collections.
We were lucky in that we were able to identify several thousand site collections that we could delete and that let us slide under the limit. (it was close)
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