VS.NET doesn't care what filename a project's assembly attributes are found in, so I'm not sure why your compiled assembly's version attribute doesn't match the project's version attribute after renaming the AssemblyInfo file.
I did a quick test here:
1) Created a new C# WinForms app in VS.NET 2003
2) Renamed the project's AssemblyInfo.cs file to AssemblyInfox.cs
3) Changed the AssemblyVersion attribute to 1.4.3.2
4) Added an AssemblyFileVersionAttribute attribute and set to 1.2.3.4
5) Built the project
Looking at the compiled executable's File version info resource (either in Explorer or a resource editor), it has the expected version of 1.2.3.4
Looking at the compiled executable's manifest in ILDASM, it has an assembly version of 1.4.3.2.
Do you get different results with a similar test, or am I missing something?
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