First, you don't need to worry about the app on app store, it will be fine.
Second, you have to download the new provisioning file in XCode for the new version. If you don't download the new provisioning file even if you set it to 'Automatic', there will be an error when you build the project.
(If you don't know how to refresh the provisioning files, see this: Xcode 7 how do you refresh provisioning profiles?)
Third, I would suggest you to choose the specific provisioning file instead of setting it to 'Automatic' because based on my experiences, xCode will select the wrong provisioning file for you sometimes.
Fourth, you have to make sure the build that you submit to app store is using 'Distribution' provisioning file in 'Release' mode. If you set it to 'Automatic', there will be a chance that it selects the wrong one for you.