Hello Steve,
Great it worked!
You are right, it is not a good idea to have both tape libraries share the same pool/media type. Mainly because LTO-6 is more than 2 generations ahead LTO-3. This means your LTO-6 drives will not be able to even read the LTO-3 tapes.
I would recommend you to have a different pool for your new tape library and redirect the jobs to use the new one, if the old one will not be used for writing anymore. You may let it there until you have useful data to restore then.
Best regards,
Ana