Basic core of both AppWarp and AppWarpS2 is same and we have made few changes (probably which you have identified) in SDK of AppWarpS2 to support the functionality to write custom business logic at server.
So, switching/migrating from Appwarp to AppwarpS2 will be a smooth transition all you should keep in mind is that there is a diffrence in SDK Initialization i.e.
In AppWarp we have following method which accepts API_KEY and SECRET_KEY
while in AppWarpS2 method accepts APP_ID and SERVER_URL
And if there is any further issue you can feel free to write back to us!