Hi Deepak,
Dirombihon is right !! What you did is just changing the the GIS-interface visualization only. The swat still has the same number of sub-watersheds.
Now you do one thing, Save as your merged sub-watershed and reach shape files with some names as two different shape files. Now you create another swat project and in place of delineation of stream network/sub-watersheds, you import your merged subwatershed and reach shape files. In SWAT, there is option of predefined stream network. It worked in my case.