Answer
This is a real limitation rather than a misconfiguration — a Base Profile (or Personal Profile) with layout/configuration entries recorded against the OLD form name doesn't automatically get updated to reference the new customized form name after deployment, since the profile's stored entries are keyed off the specific form name they were originally saved against. The confirmed workaround: export the affected Base Profile, and any affected Personal Profiles, as XML, find-and-replace every occurrence of the old form name with the new customized form name directly in the exported XML, and re-import it. Alternatively, if the specific customized screen's existing profile settings aren't critical to preserve, simply delete the old form-name branch from the profile instead and let a fresh configuration be created going forward for that screen.