The best way to change battery without power cycle

I have tried to power Pixhawk with USB when changing batteries but then I get low power warning which doesn’t disappear even when the new battery is plugged.

Is there a safe way to change a battery without power cycle - without turning low voltage protection off?

sure, just add another power input for ground power and power it using a current-limiting power supply or regulator…
for example a 4s powered RPAS, connect an external power supply of 16.8v max 2A , to power the plane. Before takeoff, I remove this ground power, and first then the freshly charged(and/or replaced) main battery is being used.

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Just wanted to comment because, as you said, the low voltage failsafe will not go away even if you change to a fresh battery.

So, if you fly a battery down and trigger the battery failsafe (either by low voltage or mAh used), you will be unable to arm the 'copter until you power cycle the Pixhawk. I ran into this issue, and I think I found the cause (from motors.cpp):

The battery failsafe is supposed to be cleared when you arm the drone (line 153), but that line is unreachable because the battery FS being on means that the preceding check fails (line 140):

139   // run pre-arm-checks and display failures
140   if (!arming.all_checks_passing(arming_from_gcs)) {
141    AP_Notify::events.arming_failed = true;
142    in_arm_motors = false;
143    return false;
144   }
146 // let dataflash know that we're armed (it may open logs e.g.)
147 DataFlash_Class::instance()->set_vehicle_armed(true);
149 // disable cpu failsafe because initialising everything takes a while
150 failsafe_disable();
152 // reset battery failsafe
153 set_failsafe_battery(false);

This seems like a bug. But anyways, I just wanted to let you know that there is still the potential of running into the same problem if you trigger the battery failsafe in flight.

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