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This helps..
What is OUTPUT_SCALE = -10800 ?
This config is for fixed motor:spindle transmition ratio.
I have 2 selectable speeds after encoder-motor
These 2 speeds are selected by hydraulic electrovalve that switches gears
position 1 max rpm is 760rpm and position 2 max rpm 3060

How to do it with only 1 button that has function cycle start / pause / resume ?

Hold on a second. I lied. Not intentionally. My spindle motor is a DYN4 servo motor geared 1:1.8 and it has a simulated encoder signal generated by the servo driver. That is the signal I am using for the coordination for rigid tapping. The sensor on the slotted plate it just for measuring RPM.
It's been a few years since I set this up and when you mentioned more slots I thought "I knew that, why didn't I do that?" Then I looked deeper and remembered how it really works.

To actually do this with a slotted plate and sensors you would want more slots and two sensors. Read up on how quadrature encoders work.

As long as you know the ratio between the spindle and encoder you can make almost any arrangement work.

These are my .ini settings.
[SPINDLE_0]
P = 2.0
I = 4.0
D = 0.0
FF0 = 1.08
FF1 = 0.0
FF2 = 0.0
BIAS = 0.0
DEADBAND = 0.0
OUTPUT_MIN_LIMIT = -5400.0
OUTPUT_MAX_LIMIT = 5400.0
OUTPUT_SCALE = -10800
ENCODER_SCALE = 4551.111111
#((2048 * 4) / 1.8) = 4551.111111
#The maximum spindle speed (in rpm)
MAX_FORWARD_VELOCITY = 5400
#The minimum spindle speed (in rpm)
MIN_FORWARD_VELOCITY = 50
#This setting will default to MAX_FORWARD_VELOCITY if omitted.
MAX_REVERSE_VELOCITY = 5400
#The minimum spindle speed (in rpm)default to MIN_FORWARD_VELOCITY if omitted.
MIN_REVERSE_VELOCITY = 50

Sorry for the confusion. I hope this helps.

Can it verify repeatedly without error?
If so if may be something related to write
(how are the WP and HOLD pins terminated?)

It's important to keep in mind that joints (machine movement) and axes (DRO values) are not the same thing. As the X axis is supposed to be perpendicular to the Y axis it would be somewhat strange for the X value to change when moving along Y.
Also note that the forward kinematic is only used to calculate the axis values from the joint home position right after homing and probably when switching kinematics. After that only the inverse kinematic model is used to calculate the joint positions for given axis values.

A little update, changed the EEPROM from a 16MB ST part to a 16MB Winbond part (same as I've used for the EPP\SPI board). Initially no change.

Put a 5ms delay between before the "sync" instruction when erasing & writing a bitfile. Was able to write a bitfile, not everytime, but when it does it verifies ok.

Ran 100 iterations of the Linuxcnc logo gcode, one after another in a loop, and then left it, after 12 hours no comms issues.

If you have nothing connected to the 7I97T but 5V power and any analog
output is not  close to 0V, the analog output circuitry has been damaged somehow.

This may occur if an output was inadvertently shorted to say +24V or
connected before a common ground was established between the drive and
the 7I97T.

OK, that simplifies things, a lot.