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There is that, but it would be interesting to see if it makes a difference, you should in theory be able to have your guide program behave a little more aggressively in chasing the errors of the mount by reducing the amount of seeing induced "error" in the system input.
I suspect that the guiding assistant in PHD might show any difference more objectively than anything else. If the long wavelength pass reduces the influence of seeing then the measured high frequency star motion should change with or without the filter.
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