Thank you for your message.
If you are using Kentico as a web site then all changes should be applied right after you modify the files. I have customized the LogonForm.ascx.cs file many times in Web site project.
Could you please make sure that you are using the LogonForm webpart? Can you try making some more visible changes? Maybe try adding some static html to the LogonForm.ascx file so that you can be sure you are using the right webpart.
Let me know if you have further questions.