If I submit app to App Store, what happens to the TestFlight build which is different version than App Store build?
Happens where? In the testflight queue? Store review/release/approved queue? On a beta tester's device?
Uploading a build involves you choosing which queue you want to put it in. If you upload a build and throw it into TF, then upload another build and put it directly to app review for release to the store, the TF build sits where it is (expired builds not withstanding).
Why do you ask?