I donβt think compiling a new set in assmebly with a different name will work - .NET will still see the same namespace - so at best you will have an "Ambiguous reference" or "Type x is already declared in dll y" , or, in the worst case, the structure will load the one that refers to that part of the application that was called first (website => 1.1, webservice => 2.0) and ignore the other.
It would be best to reorganize the application into two websites and a web service.
We have done this over the past couple of years with one of our clients - they have a huge site built on ASP.NET 1.1, but the latest stand-alone projects for them have started moving to 2.0 (3.5 under but, obviously, it is still hosted under 2.0) βWe basically had to port the common code to a new set of libraries built on 3.5, taking advantage of the new language features as we go, and we moved these sections to new websites (in IIS) as they were completed.
This is not ideal, yes, we are left with two copies of the code base (1.1 and 2.0), and any corrections, as a rule, should be deployed in two places, but this is the best way to start moving them.
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