Hi Sathish,
Your issue "Message with refcount less than 0" can be resolved by running the BizTalk Terminator tool only.
Refer this post for your issue:
Message with refcount less than 0.
The steps to be followed to resolve your issue:
Before running Terminator, always make sure you have a BizTalk Backup of your databases, all the BTS hosts have been stopped, BTS SQL Agent jobs have been disabled.
Open "Terminator" , specify server name and database information. Check all checkboxes in order to confirm that you did backup and stop all instances and SQL jobs. Find task "Repair Refcounts for All Messages"
and execute it (no parameters is required).
After performing above steps please run SQL job "Monitor BizTalk Server" and confirmed that issue resolve.