Hi Ajay,
If the configtool is showing the old information of instances , it has got two things
1. JMT phase of your migration has not been performed correctly.
2. If you are using the same hostname , SID , instance name , then it will calculate the same instance number.
In JMT phase it should delete all the information of dialog instance and calculated the new instance id
on the basis of box number calculated from the file cluster_id_switch.properties while migrating the CI.
checked the JMT folder inside sapinst_dir.
Checked the below parameter in cluster_id_switch.properties
src.ci.sid=
src.ci.instance.number=
src.ci.instance.name=
src.ci.host=
Checked the logs for java migration tool phase and java configuration parameter phase.Also do check the box number of the system.If the box number is not correct as per your input then you will not able to patch your system further.
Now in second case, If you are keeping the same hostname , instance name and SID , then it will calculate the same instance id so you don't need to worry in this case.
1644265 - "How to determine the correct box number of the instance"
With Regards
Ashutosh Chaturvedi