We have crated two applications named App1 and App2.
App1 consists of all PDF/XDP forms used within App2 which has few processes.
Whenever we modify the forms in App1, and checkin the files to the server doesn't reflect the changes. The changes will be in effect only when we deploy App1.
I don't understand why this is happening. We had another environment (JBoss) where this option was working with just a Checkin.
I believe you are getting the expected behaviour. Not sure why your JBoss environment would have worked differently.
To my knowledge, a checkin places the asset in the repository. At this point it is not available for runtime.
The deploy then places the asset in the runtime registry.
The Workbench team may be able to shed more light on this.