I have the opportunity to purchase a very lightly used M600 system for an outstanding price.

Data:
-The UAV is very clean, undamaged, and obviously lightly used.
-It comes with 4 sets of 6 TB47 batteries.

Details:
-Upon inspection of each set, all the batteries appear to only have 15 recharges, and almost no mPH have been lost, via the DJI Go App.
-I am in the process of running test flights to record the real battery life of each set.
-I plan on using this system and these battery sets to carry extremely precious cargo: A heavy Lidar Sensor.

Red Flags:
-I have reason to believe that the Batteries have not been used for ~2 years.
-One set was stored in the aircraft for that time. The battery manual says not to do this.

Is there a danger in purchasing or flying batteries that have been dormant for that long?
Is there anything I am missing?

I would suggest that you purchase a new set of batteries initially and then see if the older ones will carry a full charge and are reliable.

What @EFRPIC said. If the AC is a great deal then buy it and at least 1 new set of batteries that you can count on. The older batteries may be fine but if you're going to carry an expensive and heavy payload you'll feel better and have less risk with new ones.
Does the LiDAR payload have its own positioning or just an IMU?