As Ragul raj said, use SVN to resolve conflicts.
Go to the themesource→ right click and resolve the conflicts
Hi Sudhanshu Dhyani,
By using tortoise SVN we can able to resolve,
Go to the project directory Right click and give resolve.
Try to open the file and check for conflicts. if u think you already resolved conflicts using notepad, Go to App → Synchronize App directory to synchronize it.