Motors are step/dir controlled "hybrid steppers" that have encoder, and encoder 
feedback goes only to drivers so linuxcnc doesn't see actual position, and the 
only thing I could use is alarm signal from driver that would trigger linuxcnc 
to stop.
If it helps, this is driver used in system:
http://www.americanmotiontech.com/Products/ProductDetail.aspx?category=2&model=HBS57

> 
> I assume that in this system LinuxCNC is not seeing accurate position 
> feedback?
> 
> Can you describe the system?
> 
> One solution, assuming a step-controlled servo system where the
> encoder output only goes to the drives and not back to LinuxCNC would
> be to meddle with the normal feedback loop.
> 
> So, if you normally have
> net x-fb stepgen.0.position-fb axis.0.motor-pos-fb
> 
> Then you could have:
> 
> net x-fb-raw stepgen.0.position-fb => mux2.0.in0
> net x-fb mux2.0.out => axis.0.motor-pos-fb
> setp mux2.0.in1 1000
> net error-signal {error source} => mux2.0.sel
> 
> So, most of the time the system sees the normal stepgen feedback, but
> if the error trips it suddenly sees a bad value.                              
>           
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