Hi Rajesh,
If you migrate Folder B along with Group A then it should not overwrite security on Folder A (Which is already migrated) as it is not selected in UMT during this set of object migration. In this scenario only the Folder B, Group A (once again) and Security between the two should be migrated.
However I would recommend to test this scenario in actual DEV and QA environments before going ahead with production.
Regards,
Hrishikesh