I have two frequencies of 10MHz each just that one of them is lagging behind other by some interval.
for the purpose of measurement, i have constructed a circuit that divides the frequencies by say 32.
so will the phase difference between the older frequencies and the newer frequencies be different?
You mean you have two counters (frequency dividers)?
If so, since the counters can come up in any state at power up, so you could have 32 different alignments of the two outputs. You would have to devise some special reset logic to guarantee that the two dividers are initially in step.
Suppose your two counters change state on rising edges of their respective clocks. Suppose C2 is 1/4 period behind C1 (25ns out of 100ns). Both counters are dividing by 32. Assuming they are initially synchronized, the change of C2's output will still occur 25ns after C1, which is only 25/3200 of the period.
No, the original skew from one clock to the other clock will appear between the divided output from one counter to the other counter.
If you want two divided signals that both change at the same time, maybe you could use a D-flipflop to delay one counter's output with the other counter's clock?