Resolution:
In the deployment config enable hot deployment:
&ltname&gtbe.engine.hotDeploy.enabled</name>
&ltvalue&gttrue</value>

Hot deployment with AppManage is same as "To Hot-Deploy the Project Using TIBCO Administrator" except you are not performing the same steps using GUI but using AppManage tool. If you have made changes to .ear and want to upload without stopping the be-engine you can use -nostart and -nostop options with AppManage that will upload .ear and not restart the engine.

-nostart and -nostop will do same as this step:

10.  Uncheck these checkboxes:  
- Stop running services before deployment
- Start successfully deployed services
(When the Stop running services before deployment checkbox is checked, you see an additional setting, Kill services that haven't stopped after (seconds). It is removed when you uncheck the checkbox.)

Did you try this and did it not help.

[tib55@linux4akhan bin]$ ./AppManage -nostart -nostop -deploy -ear ~/FraudDetection.ear -deployConfig ~/FraudDetection.xml -app FraudDetectionRepo -domain domain55_linux -user admin -pw admin
Checking if master server is responding ...
Finished checking
Initializing ...
Finished initialization
Loading archive ...
Instance Name is : domain55_linux-FraudDetectionRepo
Finished loading archive
Configuring application ...
Finished configuring application
Deploying application ...
Finished deploying application
Finished successfully in 56 seconds