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Could you explain me better your idea?
Is it non feasable for you to correct the phase during normal working?
Let me know.
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An NCO has clock enable input. If it is enabled then it starts and works as long as it is enabled and will start from zero phase(by default).
So if you have a sync pulse then wait for it in each fpga and assuming they arrive at NCO at same time then both NCOs can be enabled together from zero phase. All you need is convert that sync pulse to high signal starting once sync pulse arrives. Then the two outputs will go to DACs I assume and again delay issues may arise which you can measure and adjust digitally to within your available clock resolution.
You can also allow both to run freely then correct phase if you get copy of one fpga output to the other but this is overkill. You may also have ways to align in the analogue side but that is not my territory.
If your system is reliable you can also just measure the default delay and correct the phase in one fpga by offset if available on your nco or by starting one nco under control of clock enable.
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