Plug main drain & revamp plumbing

Is there any risk if I end up draining the majority of my pool?
Only if the pool drains lower than the groind water level. Then the pool starts becoming more less pool and more boat. Plenty of places have deep ground water and they're fine.
The pad is not below the entire pool depth.
Hopefully your estimate was only an inch or 2 two high and it fixes itself. (If not already)
 
So I dove my pool & removed the floor inlet cover. It's the standard Pentair 08417-0005. I was surprised to find the plugs I had would not work to stop up the inlet. The threaded ones I have are too small and the rubber plugs don't work because there are nipples around the hole below the threads preventing those from taking a seat. Anyone know a part number for a stopper that can directly screw in those threads to block the inlet? Gonna try Pentair R22011
Just FYI, the Pentair R22011 winterizing plug seems to fully stop the inlet that takes the Pentair 08417-0005 cover
 
How big of a deal is it to have the Polaris booster pump feed after the salt cell? If I set everything "properly" I will have a section after the heater where I have the booster pump feed, flow sensor, check valve then salt cell. That will have to be a long run due to minimum required straight run before the flow sensor. Although I do think you can get away with less than 10".