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The pin for the inverted state would be 'hm2_7i76e.0.7i76.0.0.input-29-not'

Try and use the pin 'hm2_7i76e.0.7i76.0.0.input-29' in your hal instead of 'hm2_7i76e.0.gpio.029.in_not'

Using LINIXCNC 2.9.2 on Debian 12 in combination with a Mesa card 7i76e. Both limit switches of each ache are setup in parallel (LJ12A3-4-Z/BX  like NPN) with a pull-up resistor of 100k ohm. My Aches are attached to mesa digital in X => 27, Y => 28, Z => 29. The signal has to be inverted because is up if the limit switch is not used. So far so good. Now configuring my LINIXCNC to have a shared both limit and home together.net both-home-z     <=  hm2_7i76e.0.gpio.029.in_not
net both-home-z     =>  joint.2.home-sw-in
net both-home-z     =>  joint.2.neg-lim-sw-in
net both-home-z     =>  joint.2.pos-lim-sw-in
 The INI contains this settings for the Z-archesHOME_OFFSET = 0.0
HOME_SEARCH_VEL = 2.000000
HOME_LATCH_VEL = 0.500000
HOME_FINAL_VEL = 0.000000
HOME_USE_INDEX = NO
HOME_IGNORE_LIMITS = YES
HOME_IS_SHARED = YES
HOME_SEQUENCE = 1
 Now to the issue, if I home the machine the limit switches get ignored. This applied to all aches. To simplify the troubleshooting I focus on Z-aches only. If I use a piece of metal and hold it in front of the limit switch the mesa digital in 29 acts as expected, but not the chained signals.

Any advice are welcome.

DAMN!!!!
That is 99 degree C all cores all the time, no wonder the PC is giving up it's ghosts, slowly and painfully!
The good thing is, you have it easy to remove the CPU cooler and clean both the CPU and cooler, then find some thermal paste and apply some to the CPU and mount the cooler back.
Tooth paste works instead of thermal paste, albeit for a day or two only.

sensors at the time of error:
 
Also this is how I have my pc mounted with plexiglass. Should I holesaw a vent for it through the plexiglass?