I replaced the whitespaces in my application names with underscores "_" - Customer_Application. I had a similar issue when my server start script read the conf file with the application name system property and after wasting several days I decided I would be better off avoiding more trouble down the road by getting rid of the whitespaces now.
When you move your nodes to the new app, the business transactions statistics are available in the Metric Browser at the tier level but you will no longer be able to drill down to the node level.