CR application fails with 'Server did not respond' error

Document ID : KB000111491
Last Modified Date : 30/08/2018
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When applying CR to API Portal, it sometimes fails with the following error.
  'Server did not respond'
What is the reason for "Error: Server did not respond"?
API Portal 3.5
The 'Server did not respond' is indicating that the applying of the patch took longer than the current maximum of 500 seconds. 
CA will increase the timeout for the next CR. 
The recommended workaround is to remove the .done file in /opt/Deployments/lrs and repeating the upgrade.