What to do if I worked for a company for 5 years and they are saying I never worked for them when jobs call for a referance?

If your former employer is refusing to acknowledge that you worked for him, her or it for five (5) years where you want some reference for some job applications, then you are caught in a difficult situation. I would state in the applications for employment that you worked where you state you worked and be prepared to provide a W-2 to show that you actually were an employee of any such former employer that is denying that you were employed.

The problem I see is you are not going to get a decent reference from your former employer from what you have written.