Bart_Veltman finding suitable stars for autofocussing is not always easy
Binning works fine as long as you focus with a Bahtinov mask. Not so good by focusing using star sizes (HFD or FWHM) if your plate scale becomes undersampled after binning.
In general, the trick is to move to a bright star to do the focusing. Then move to your target after focus is achieved.
If you are using a filter wheel or filter drawer, and you can easily swap filters, another way is to use a Bahtinov mask to focus very carefully with a filter that lets through more light, and note down the EAF steps. Then, using the bright star, focus with your more narrow band filter. Again, note down the EAF steps. Take the difference between the EAF steps and write this down in your observation notebook. This delta EAF step number is a constant (even through temperature changes), and should stay the same as long as you keep the same OTA, same R&P focuser, and same set of filters.
Once you have the delta, in the future, just use the Bahtinov mask with a broadband filter to focus a star, note the EAF step size, and apply that delta to move the EAF directly for your narrower band filter, without having to focus with the narrow band filter.
You must get rid of backlash when you do the above. One way to avoid backlash is to start at say, 400 EAF steps to the high side of the focus, and using the Bahtinov mask, approach the focus only by reducing the EAF step size. If you overshoot, go back to the starting point again, and try to achieve focus again; always moving only in one direction.
Now, do the same with the narrow band filter, while you have a bright star -- start at some point that is a few hundred EAF steps higher than the focus location obtained by applying the delta, and do an EAF GOTO directly to the computed location.
William Optics sells plexiglass etched Bahtinov masks that are very bright, compared to the standard laser cut (or 3D printed) masks.
You can obtain the correct delta without actually measuring as long as you know the draw tube movement per EAF step (easily measured), and you know the thicknesses of your filter glass. For most optical glass, the delta distance is close enough to one third of the difference between filter thicknesses. I.e., if the narrow band filter is 3mm thick, and the wideband filter is 2mm thick, then the draw tube needs to be extended by an extra 0.33mm if you focus with the wideband filter and take images with the narrowband filter. Knowing the EAF step size scale (usually of the order of 4 µm per EAF step, but it depends on your rack and pinion focuser), you can then compute delta in terms of EAF steps.
Chen