Jaswin, you are not being very clear. It is hard to understand you.
This might not be right answer.
The purpose of deleting stories is not to "solve" your problem. It is to isolate the problem with the document so you can perform other operations on it. Think of it as a diagnostic.
If I need the xml content, I have to place it in pasteboard.
This is not a normal requirement. Normally you tag XML content in the actual document, not on the pasteboard. Why are you doing it this way?
But furthermore, you said earlier:
Even If I tried after removing the pasteboard contents I get the same issue.
So if the corrupt story in some of your other documents is not the XML tagged story, then you should have an easier time repairing it. For instance, by exporting the text in the story to InDesign Tagged Text.
But you're in uncharted territory with a rare workflow involving obsolete software, so I don't know how much more we can help you. Certainly it would be a lot easier if you made it easier for us, by explaining more clearly and answering a bit more promptly.
