As you note, synchronisation will present the fewest difficulties for your work. The question "how many difficulties will be caused by lack of synchrony" is difficult to answer. The answer depends upon what you are trying to address with your surveys.
Do you wish to make temporal inference separately for the two areas? Are you trying to make spatial inference between the areas over time? Is there sufficient effort and adequate detections within each area that they can be "self-sufficient" or do the data need to be pooled across areas to obtain sufficient detections for fitting detection functions?
I don't think there is a simple answer
regarding the threat to the robustness of the results. But the
questions above form a sort of 'checklist' I would use to
formulate my ideas on the subject.
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