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Avoiding feedback loops in AD9545/AD9546 system clock compensation

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Product Number: AD9546

I have a setup with a low-frequency (100 Hz) synchronization marker embedded in a high-frequency (10 MHz) clock reference locked to GPS. I would like to use the high-frequency reference for system clock compensation, in particular to measure skew using the skew measurement unit between the tagged 100 Hz synchronization markers on various inputs to the AD9546, including the input with the high-frequency reference clock. This seems like it involves applying compensation to the TDCs associated with the synchronization markers based on the high-frequency reference being measured by the same TDCs. This seems like a recipe for a feedback loop. Is there an obvious solution to this that I am missing?

Clarify wording
[edited by: nwhitehorn at 4:49 PM (GMT -4) on 15 Sep 2022]