If my customer had an Adobe VIP with several licenses and accidentally set up a new ADOBE VIP then can they still access the licenses under their old portal?
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Yes. The older licenses, if still valid, will continue to remain accessible. It's just that Admins (if they're admins on both orgs) will need to switch the org in the Admin Console.
For the users:
If your orgs have been upgraded to "Storage for business" a.k.a have a Storage tab in the Admin Console, there may be some changes in the experience.
As the users will now be Business ID users, they'll need to choose a Profile at sign-in. And can only be signed in to one profile at a time on the same computer. So, if a user has product assignments on both the consoles, their sign-in experience will change a bit. See Intro to Profiles.