I have recharged the angle valves, I still get the thumping noise after each toilet tank is refilled after flushed. This noise only happens when the toilet tank is finished filling and not when a sink tap is closed. The angle valves and flex hoses from tha angle valves are new. All water pipes have been exposed and re-secured to wall studs. The noise does not appear to be coming from the ball cocks. I have tried just about everything and have now run out of options. Your assistance is appreciated.

The thump is likely air hammer. Has it always done this, what kind of fill valve is on the toilet? You could replace the fill valve with a Fluidmaster 400A for under $10 and the problem will likely be gone. What did you mean by recharging the angle valves, do you mean an air chamber inside the wall?

You might try partially closing the angle valve to restrict the water flow into the tank fillvalve of the toilet and see if that reduces the hammer affect.

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I have recharged the angle valves,

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Did you follow my directions when you did?
Back in the 60's we were required to to put air chambers on all bath lavatories and kitchen sinks. Over time water and condensate built up in them and they must be recharged. First turn off the house at the main house shut off valve. Then open hot and cold faucets at the farthest bathroom to prevent air lock.(This is important.) You will find under each fixture little brass or chrome valves. These are called angle stops. With a small pail held under the angle stop to catch the run off look under the handle of the stop and you will see a nut with the stem running through it. This is called the bonnet packing nut. Put your wrench on it and back it off counterclockwise. Now open the stop and remove the stem and washer assembly, The stop will began to drain. When it has quit draining reassemble the stop and move on to the next one. Do this on each one of your angle stops. There will be six of them in a two bath home. When you are done, close off the faucets you have opened, turn on the water to the house, and give yourself a pat on the back