Can you try this:
1) Select the application.
2) Right click on the application and select 'Delete'.
3) Select 'Yes' for 'delete local copy of application and it's assets'.
Do not check the option - Also delete the application from the server.
4) Now go to File.
5) Select 'Get Applications'.
6) Select your application and click 'OK'.
You should be able to get the copy of your application which is on the server. Checkin and checkout should work fine after that.
Let us know if the issue is still not resolved.
The steps mentioned above did not resolve the issue.. We also tried to restart the server multiple times but no use.
Can you please also share the workbench log file ? Go to Help -> About Adobe LiveCycle Workbench ES4 ->Installation Details -> Configuration tab.