Hello,
I think I don't fully understand what you mean. Are you aligning an oscillator so that it has (almost) same frequency as some other master or reference, and after the alignment, there is no link between the oscillators (so a PLL is no option)?
When this is the case, you could use a frequency counter, but another way is to use mixing (frequency beating), or a dual channel oscilloscope. What is the maximum allowable frequency offset between the two devices?