You are smart to start separating your code into multiple projects. This makes that development, deployment, and managability of your application much easier. I have seen the My.APplication disappear before but the cause is generally from moving code from an application to a class library....but not always.
I would have to actually get my hands on teh project to give you a definitive answer. One thing is certain though...pretty much everything given through the My.Application reference can be retrieved a different way.
Pretty much
In regards to your project, do you have any of the other "My" references such as My.Computer? Without getting hands on I am not sure I can give you a very good answer here....sorry