I have a 2 story town house with a tankless water heater and PEX pipes. First year was fine. Start having issue the second year. Low pressure on the hot side. The master and kitchen. We found tiny pebbles and rocks in the aerators. We clean them and flush the system the first time, it was fine . Then low pressure again in a couple of months. Call the plumber. He found larger pebbles in the valves. So did another flush, changed 6 valves and kitchen faucet. It was ok for another 3 months then low pressure again. Call a different plumber, he did a flush again and a month and half later we have low water pressure again. Plumber checked the unit and it is fine and the pressure from the unit is good. One plumber said it is calcium deposit and another believe it is rocks. During the time span when we first discovered the pebbles in the aerator the city did do some work but not sure if that affected our house. Non of the neighbors have water issues. Plumber has suggested repiping, change back to tradition tank water heater, filter. All this occurring over a year span. Any suggestions. Thank you in advance.

why not install a filter before even thinking about changing anything ?

Agreed with Packy. If the filter clogs, cut it open, dry it out, and examine the debris. That's what's coming down your water main (but no longer clogging your fixtures!)