Q.
Can I use the square wave at 50% duty cycle to sync with the ADP1047/48?
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A.
That would work fine. Sync works on edges of the pulse, so as long as the pulse is a clean edge and the pulse width is no less than 120ns you can use any duty cycle.
The controller will sync to the external clock, as long as the period is within +/- 12.5% of the internally programmed clock period.