dushmanta_kiit,
Can you give me some more details of the issue that you are facing. What do you get this message? While saving a file or while closing the IDE?
Could you go to MyEclipse > Installation Summary > Installation Details and paste the information here for me.
Have you tried using the -clean command to fix your workspace?
https://www.genuitec.com/forums/topic/troubleshoot-using-the-clean-command-line-argument/