Flex 4.5 is not supported by Flash Builder 4; you will need to upgrade to Flash Builder 4.5 to take full advantage of Flex 4.5.
I did notice unexpected compilation and run time error while working on the same environment.
Do you think Adobe will fix this incompatibility issue for FB4 ?
No, I don't think so. FB 4.0 + Flex 4.5 is not a supported configuration and is not tested.
So if I like to roll back my application from 4.5 to 4.1 SDK, can I expect Backwards Compatibility Issues ?
That depends entirely on what functionality you are using in your application. I would expect that if there are any issues, they'll become immediately evident the first time you try to compile against the 4.1 SDK.