The new TICC support in Lady Heather has an "autotune" function that can null 
out the cable and channel delays.  You connect a signal (like 1PPS) to both 
channels through matched cables (like via a T adapter) and it averages the 
difference and sets the "FUDGE" factor for one of the channels to null out the 
net offset.  It doesn't null each channel individually.    You might be able to 
swap the cables and work out how to allocate the offset to each channel.    My 
unit has a channel offset of -305 ps (part of which could be due to mismatches 
in the "T" cables / connectors).

Autotune also calculates the FIXED TIME2 values if you want to play with that 
feature which can allegedly reduce the device noise by sqrt(2).  I'm not sure 
how well that works since the TIME2 values do drift over time and I don't know 
how much of an error in the TIME2 settings affects the device enough to make it 
perform worse than with the default automatic TIME2 mode.

---------------------

>  The whole delay difference thing does get into a “do you care?” sort of 
> category. The 
testing process you are doing may well calibrate out (or ignore) an offset of 
this nature. 
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