Thats true but how the folder level comparison will take place? if the objects are too many suppose 200 objects in one file and 150 in another, i could find 50 object difference but which 50 how can we get it?
"Thats true but how the folder level comparison will take place?"
I don't know. That depends on the tool you use to compare files in folders.
Remember that in a binary QVW document every Object is uniquely identified by an Object ID. This ID is reflected in the XML file name in the -prj folder. For example, compare file CH123.xml from the first document to file CH123.xml from the second document to find out which object properties have changed. The 50 objects in your example that have no counterpart are probably new objects or deleted objects and cannot be compared to anything.