So i got this working by following this link.. 
https://groups.google.com/forum/#!searchin/google-appengine/cname$20settings/google-appengine/X6N80msPbl8/rwKwOm-tJ_oJ

Thanks to the community! :-)

On Saturday, August 17, 2013 4:25:40 PM UTC+5:30, Sumit wrote:
>
> Hi,
>
> I've been using the legacy master-slave datastore for my application (lets 
> call it oldapp) and have migrated the same to high replication datastore by 
> creating a replica (lets call this newapp) as recommended by Google! Now 
> i've a challenge to redirect my domain to this new instance. Let's say my 
> domain name is foo.com and www.foo.com. I use whois.com domain services 
> to map my domains to appengine app instance by mapping each of my domain to 
> ghs.google.com via CNAME entries. Now when i'm trying to add foo.com as 
> domain in "newapp" appengine instance, it's failing by giving me an 
> "Invalid request" error. Literally there is no other information and the 
> page that appears is completely blank. Any idea how to go about this 
> migration?
>
> Thanks,
> -Sumit
>

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