The SDK of BizTalk 2006 Beta2 will include a new version of the adapter base classes. These will not be backwards compatible with the original BizTalk 2004 SDK classes.
The API has changed and the internals have changed (uses System.Transactions for example). Adapters that have been originally built with the 2004 adapter base classes should continue to use and be deployed with this version.The .NET1.1 compiled assembly of the old base classes should by default work with.NET2.0 CLR.
You could of course prefer to re-compile for .NET2.0 but you will get some warnings during compilation time.