I have an app on app store, which is using an iOS Provisioning Profile (Distribution) which is invalid. This Profile contains Push Certificate.
so I want a regenerate
As you mentioned in your question that Provisioning profile is Invalid. So i guess certificate is expired & you are going to renew it.
If so than yes current app store version will work fine. If you update provisioning profile by new certificate it will not affect current App store version at all.
I hope this information will help you.