I have 2 distribution Provisioning Profiles,both has the same App Id
Profile 1: using which an app was already in app store
if I upload an ipa to itunes using Profile 2(same App Id), will that update my old app(which was uploaded using the Profile 1) in the itunes?
No, it won't change anything and will successfully update your app if the
App Id
is the same. It doesn't matter how many Provisioning Profiles you have for the same app.