Bricks, Masonry, Asphalt and Concrete - Flagstone: repair or replace

I have a 30+ year old 8x15' flagstone entry that is started to crack out. There is about 1/3 of the area loose with the grout and mortar backing broken out. You can tell the plywood underneath is not as stable as it should be on that third. The base is seperating on the lath, would it be smarter to try to repair this mess or just replace it as a whole? And would you recommend using cement board or doing it the same way it is now? I am not 100% sure on the thickness of the mortar i need to pop out one of the loose flagstone and drill it to check. The plywood underneath is a single layer of 3/4" which seems to need to meet my framing nailer and some ringshank nails.

Cracked grout and cracked tiles or stones are a sign of movement in substrate. Concrete underlayment board is recommended. Any movement in substrate tends to result in cracked grout and possibly tiles and stone. Make sure your joists are adequate and provide proper support to subfloor.