Answer
Yes — Appearance Configurations are copied as part of a clone (the underlying data lives in fnd_model_data_tab, cloned alongside page configurations generally), so any environment-specific appearance differences (like a distinct logo per environment) get overwritten with the source environment's settings every time a clone runs. A documented post-clone step — reapplying the target environment's own appearance configuration and swapping the Document Logotype back to that environment's distinguishing logo in every company — is the practical way to keep this environment-identifying setup intact across repeated clones, since there's no way to make it clone-immune on its own.