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It will inform you that the correct procedure would be to perform the upgrade at the Central Instance / Primary Application Server, and that all DIs / AASs have to be uninstalled and re-installed.
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This is not correct. The application servers are uninstalled and reinstalled only in case of Java stack and in certain cases like release upgrades. There is no need to uninstall and reinstall the application servers for ABAP stacks during an upgrade. There is an option called "Update Dialog Instances" available in the SUM tool which should be selected so the tool will make necessary modifications to the profiles of the application servers. If this is not selected then you will need to manually make the changes.
>>We have upgraded QA and Dev in the parallel environment. We need an additional application server for parallel QA so user can do their testing. Our support landscape has 2 addional application servers in QA. We are taking one from existing and adding to parallel QA.<<
The reason why I provided the steps to install an application server is because of the above statement from you. If you have not selected the option "Update Dialog Instances" during the preparation phase then you will need to check and update the profiles manually. Based on what you have said, you updated the system from ERP 6.0 to EHP6. As part of the update I believe the start profiles get merged with the instance profiles. So first check if the profiles were merged for the primary application server and if yes then you need to do that manually for the application server instance. Once done check if the AS is working fine.
1528297 - Merge start profile with instance profile
1898687 - Merge start profile with instance profile (Linux/Unix OS)