The idea behind encoders is the relationship between the A & B channels. They can have 4 different states: 00,01,10, & 11. That's why they refer to this as quadrature...(4)
Also, the extra channel (Z) is typically a homing pulse, which occurs only once each rev.

You mentioned the encoder had 500 pulses per rev. as did the stepper.

500 pulses per rev is an unusual number for stepper motors. Microsteppers are typically some whole multiple of either full or half step steppers, which are usually 200 or 400 PPR. Numbers like 1000, 2000, 4000, and so on are typical for microsteppers.

Regarding the encoder, is it a 500 line encoder, or does it actually generate 500 quadrature pulses per rev? If it is a 500 line encoder, then there will be 2000 quadrature pulses per rev.

You mentioned you are only looking at the A phase as a test. This will tell you the number of lines on the encoder disk per rev, and if you multiply this by 4, you will have the quadrature pulse count per rev.

If possible, can you tell me how many revs you completed to achieve the 23000 pulses? Or maybe, could you find out how many pulses are in a single rev by measuring.

One more thing: When controlling an axis with a stepper, and using an encoder as feedback, the encoder should be coupled to the actual thing rotating, and the motor can be remotely connected via a belt or gear box (anything with lash). In your application ( a linear stage ), the encoder should be a linear encoder, coupled directly to the stage, not to the motor, the lead-screw, or anything else with lash.