If you are creating your application in ASP.NET 2.0 you should take into consideration that the assembly names are generated automatically on each build by default. Db4o distinguish persisted classes by name, namespace and assembly. So after the assembly name has changed, you won't be able to access classes saved with the previous version of the assembly.
There are several workarounds:
aspnet_compiler.exe -v /WebSite -f -fixednames c:\WebSite -c -errorstack
Microsoft has published a how-to for using the aspnet_compiler to generate fixed names for ASP.NET assemblies.
You can use TypeAlias for aliasing only specific class.