Although copying the Thingworx Storage is a nice quick way to move your development, we recommend.
1. Install new instance
2. Install all extensions on the instance
3. In old instance export all to Thingworx Storage
4. Copy export from ThingworxStorage/exports to new instance
5. Import all from Thingworx Storage
Thanks for your repose. I did stop the tomcat. The issue was even though it is same release, the installations are from different builds. I copied the source war file to target location. everything started working.
I agree the better way would have exporting and importing everything. It is long process as well there was possibility that some extension may not work.
Anyway, I got around this problem.