1. List the address that she worked at in the form. Additionally, it can't hurt if you add a separate page mentioning that the company now can be reached at a new address.
2. Do what you find the most reasonable. For the reference the most important thing is that it's a person that can, with some authority, confirm her claim that she worked there. So anyone she reported to and remembers her name is a good choice. I would say manager from Y is a good choice. Again, if you want to avoid confusion over X and Y, simply add a short (!) explanation on a separate sheet.
Thank you Spyfy. you are right in saying that it never hurts to add a short explanation. I will add extra sheet to explain the scenario.