After some time the following screen appears.
The Application on Bluemix is NOT started. Only after a refresh the application on Bluemix is running again. I have submitted a question on this subject on IBM developerWorks: Time outs deploying change using Domino Designer.
The answer by Gary Marjoram:
When the deployment process enters the "Waiting for application to start" phase, Designer is polling Bluemix every 5 seconds to check if the application has started successfully. Designer will poll Bluemix for 180 seconds by default before giving up and displaying the error Dialog you've shown above. Typically Bluemix takes somewhere from 90 - 150 seconds to stage and start an XPages application, but it may take longer if Bluemix is under heavy load. In your case the application has started after the 180 second timeout, which is why you got the error Dialog but the application appeared to be running when you went to the Bluemix Dashboard.
There are two ways to solve this.
1. You can extend the amount of time Designer will poll for in the Bluemix preferences.
2. You can disable the "Waiting for application to start" phase of the deployment process completely.
If you do this Bluemix will still stage and start your application but you will get no indication in Designer when the application is ready.
In my situation, I changed Timeout (seconds) to 360 and the messages were gone. My advice is NOT to disable the "Waiting for application to start" phase but to increase the Timeout setting (seconds).