When using descriptor heaps and the "legacy" descriptor mechanisms in the same frame, my understanding is that the non-heap bindings clobber heap bindings and vice versa. It does not appear that the validation layers detect this - I would expect to see validation errors in either direction (using pipelines that use heaps if heap bindings have been invalidated, as well as using pipelines that don't use heaps if non-heap bindings have been invalidated).
This is using Vulkan SDK 1.4.341.1 - unsure if this has already been addressed after the SDK got released!