If you've already modified your generated classes, I think you might find it easier to do with Visual Studio's global replace with a fancy regex to find the classes you need to change. (If that's not possible, it's not hard to write a quick console application to process the files).
Using T4 you can control which files are overwritten, for instance using the Output.PreserveExistingFile
which comes with T4 Toolbox.
<#
var t = new SampleTemplate();
t.Output.File = "Sample.cs";
t.Output.PreserveExistingFile = true;
t.Render();
#>
And then you can delete the specific files you want recreated. But however you determine which files to overwrite, any changes to those files that you've made since last regenerating will be lost. One recommendation is to build your templates as partial classes so that you can put all manual modifications in a separate file (but that doesn't really help you if you've already modified your generated classes).