jpeardm,
Check valves are used between the spa return and pool return lines when the spa water level is higher than the pool water level(i.e. raised spa).
I've seen some bypass systems with infloor cleaning systems because of poor design.
It would be helpful to have pictures.
Check valves has no pressure reducing purpose.

thanks for the reply, Further info is that the spa is at same level as pool and there is an open balancing pipe between the two. The photo shows the check valve on the right with pipe above that was tee'd into the supply to the heater just after the filter. It is then tee'd into the pool returns after the Jandy 3 way for caretaker/pool return choice.

Another photo.

Generally, you would need one 3-way valve on the suction side of the pump. This would separate the pool suction(skimmer and main drain) and the spa suction. And there is usually one 3-way valve on the return side of the pump. This separates the pool returns and the spa jets.
It appears, IMHO, that the plumbing was done without much forethought about the equipment function.
I would say the check valve is there to prevent the backflow of water thru the heater if the valves are turned in the wrong direction.
Do you know why you have a 2-way valve in front of the pump? Is the equipment substantially higher than pool?
In the second pic, what is the ball valve for? Do you have a suction cleaner?
If you are going to replumb the system you really need to get help to configure it correctly and efficiently. My guess is that there was a flow problem when they started things up and they made changes to make things "kind of work".
Good luck.

thanks again for the reply. Overall the system has worked nicely since new in 1996 so no complaints there but just wondering if I should plumb in a new check valve at that location. The line with the red handle ball valve was for a suction cleaner which now is used for some Magic Stream Jets using a separate pump. That piping is all redone now since these photos. The 2 way in front of the main pump was to help hold prime while cleaning the basket but really isn't necessary anymore with the Intelli-flo pump I use now primes easily.
I appreciate your thoughts on this and taking time to answer, thanks.