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I had similar problems with my toolsetter, and initially used an AND gate - until the time I forgot to enable it (I used a manual signal, not motion.*) and crashed my toolsetter.  Then I tried smoothing, which worked OK.  It turns out the toolsetter is a good seismic monitor, and trips when I have issues with toolchanging

However, my comment here is... have you considered using a dummy probe move to retract the probe?
 

Cheap chinese magnetic encoder E6B2CWZ6C, 2500 P/R (10000 quadrature counts), spindle speed ~1400 rpm at left and ~60 rpm at right. Halscope shows velocity in rotates per second.
 

This is indeed a much neater method, great! I also solved it quickly and durty with an AND gate. But creating your own component is much nicer in the Hal code.
If I have an evening off, I'll play around with creating a comp.

Which LinuxCNC version? Not that it probably matters as I don't see much difference in this area.

I think that the dialog box is created here:
github.com/LinuxCNC/linuxcnc/blob/master...cripts/axis.py#L1643

With some TkInter stuff in the backgorund that I don't really understand.

But, I don't see where "file not open" comes from. There isn't normally anything in that area of the dialog, I don't think? (unless you know better?) so I can't even find a hint of which file isn't open.