I don't think you can change the assembly version once it's been compiled. Although you can compare the assembly versions of two separate dll files.
string existingAssemblyPath = "foo\\bar.dll";
System.Reflection.Assembly existingAssemby = System.Reflection.Assembly.Load(existingAssemblyPath);
Version existingVersion = existingAssemby.GetName().Version;
byte[] downloadedBytes;
System.Reflection.Assembly newAssemby = System.Reflection.Assembly.Load(downloadedBytes);
Version newVersion = newAssemby.GetName().Version;
if (newVersion > existingVersion)
{
}