I have paused and resumed a print from the control panel on the printer and it picked up no problem where it left off.
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It should be homing the z axis as well. I wonder if the z endstop is mucked up.
When you pause, it homes to min x, min y, and max z.
What you are describing does not sound like it is hitting max z.
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Try printing out two spacers to raise extruder 1/4" and leave z stop in factory location.
