Citrouille57,
To test, I have created a test enterprise application project with a web module and EJB module.
TestEP
|
|__ TestEPEJB
|
|__ TestEPWeb
I am able to deploy TestEP, TestEPEJB and TestEPWeb separately. All you need to do is right click on the module -> MyEclipse -> Add/Remove Project Deployments. If your deployment is already existing, selct the deployment and click on [Redeploy]. Else click on [Add] to add the deployment.
HTH!