Dear Kashif.
250+ lock entries isn't that many in a system that by default can hold up to 30.000 locks.
The locked transaction was caused by an exclusive lock, can be identified by LOCK MODE = E.
Never delete lock entries manually, this will always cause problems.
Instead you should identify the user/background job creating all these exclusive locks and end their process either in SM04 or SM50.
Thereby the system will clean up automatically and you would not have any inconsistencies in your system.
Regards,
Teddy