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Our company is CMMI level 3 certified going for level 4. I would like to
know if there's a way to audit the automatically generated .net files for
release management and versioning.

Normally we have our source code as class files and we generate exe’s and
dlls out of them and send for system test and to production further on.

So, we never send our source code to systems and we only send exe’s and
dlls. I want to know the right process on auditing such kind of
applications. I am not sure whether auditing those exe’s and dlls that
really goes into system test? OR the class files that has the source code?

If you say class files, then we may have to deploy source code also in
system test but that may raise security concerns.