Hi Thamil,
That is exactly the reason for the 'loss' of data. The full name of any agent takes into consideration the domain name, so the historical data of the agent under SuperDomain is not the same as under a custom domain.
There is no way to resolve this in the way that the product is designed, the data from the two agents will be considered distinct, at a data level, they are considered two different agents.
All of the data is technically still there.
If the agent was mapped back to Super Domain, you would see the historical data again for the agent, but of course it would be mapped back to the SuperDomain, and you would have a gap of a few days' data while the agent was mapped to a different domain.
Thanks,
David