If I have published 2 channels in one developer ID.(same key and same password).I have stored login details of channel 1 in roRegistrySection and some other details of channel 2 in another roRegistrySection.
My requirement is When user will remove channel 1 ,then only channel 1 roRegistrySection will be cleared. And if the channel 1 roRegistrySection Data will be cleared then the channel 2 roRegistrySection will remain unaffected.
For your second package rerun genkey again - and make a pkg for that one.
Then when you're working on each app, 'rekey' the box before you make a pkg file in the future so the key will be correct for that registry set. To avoid the hassle of this though, if you only have two apps, it would be easier to get two rokus - that way when working on app A it's always loaded on roku1, and app B is always on roku2 with the correct keys.
(Or Eclipse I believe keeps the keys in order for each app)