During a recent restart of our development server the SQL Server
started using .NET 4.0
for the SQLCLR. This means that nothing using the CLR in SQ
They made explicit choices to ensure that installation of .NET 4.0 would be non-impactful. It shouldn't be using .NET 4.0 or any of the new files except for the new shim files, mscoree.dll and mscoreei.dll. Those should be backward compatible with the 2.0 runtime. You could run Process Explorer to see the version numbers of the dll's loaded to verify that it is running the right runtime.