Hi Ganesh, You didn't followed wrong procedures. Each document (Domain model, Page, Microflow, etc.) in the Modeler is an element in the subversion control. Mendix will always try to merge documents from a branch-line to a main-line. I don't know what is changed in the main-line between the creation of the branch-line and the merge you try to execute now. But a movement in the domain model of a random entity is also considered a change of the domain model in Mendix. When you delete the object in the branch-line and change it in the main-line, subversion can't merge the changes and decide always to revert the deletion in the merge. Yes, this will give you errors in the rest of your model because the changes doesn't match anymore with your domain model.
I hope this give you some info on how Mendix works.