Here's our scenario.
We successfully migrated our SharePoint 2010 Foundation databases to another server using this method and this article. The key point is that we set up an alias from our existing SQL Server (let's call it "SQL1" for this post) to the new SQL Server (let's call it "SQL2") for this post, per the best practice in the article.
The problem is, we have some custom databases on "SQL1" that are used by web parts (don't ask why: legacy code). Those web parts look in the web.config for the original SQL Server name "SQL1", which now has an alias on it.
Since we only migrated the SP environment databases, these custom DBs weren't moved, so now we get errors saying that the custom databases could not be found, because the alias points to "SQL2", where the custom DBs don't exist. How can we get around this without moving the custom DBs? Is it possible to add multiple aliases on "SQL1" to point back to itself (sounds crazy, I know)?