Sounds like you should not have stopped "flushing the system". You don't have a lot of options with sediment in the well. The first thing to do is try to pump it clean. You have to use more than just a hose. You have to open up a big line or run several hoses to get the pressure down and the volume needed to bring the sediment out of the well. You may have to pump it hard for days to do any good.
If pumping it out doesn't work, your next option is to pull the pump. Then you can have someone treat and clean the well, or run a camera to see what the problem is.