This is the correct answer! AF does not work well at small apertures. I had the same problem with a Nikon 80-400mm lens. Take the filter out and it AF works like a charm.

I have done too many indoor events like that and the settings depend on the light in the church at that time.
First of all, forget big lights with umbrellas, softboxes, etc. They are cumbersome and the people will move, get off center, etc and will give you more problems than solutions.
You need a camera body, D810, a lens, 24-70mm f/2.8 and a flash with a white diffuser, I use Nikon SB910 and the system never failed me.
If you have a second body, use it with the 70200mm lens and another flash. You will not have enough time to change lenses in occasions like these.
Regarding the settings, you have to experiment maybe an hour before the event to get the right settings.
Shoot on manual mode, NOT Aperture priority, because the light is uniform inside the church.
Aperture f/5.6 for individual shots or when they are in the same focusing plane. F/8 or f/11 for group shots with more depth.
Shutter speed between 1/100sec to 1/200sec depending on the focal length of the lens and subject movements.
The ISO depends how bright or how dark you want the background. This is why you practice an hour before the event. Remember, the luminance of the church background depends on the shutter speed and ISO.
The aperture will control the luminance of the subject given the flash output. Take some photos of the people at different distances from the camera and when you find the distance that the exposure is right, then keep shooting at this distance for the duration without changes in the flash or other settings. Zoom in more for individual shots and zoom out for group shots without changing the distance between camera and subject. This is why a zoom lens comes handy here.
If the background is dark, increase ISO and/or decrease shutter speed. The opposite if it is too bright.
If the subject is too bright, go from f/5.6 to f/8 or f/11 or reduce the flash output or move back a little.
It takes some practice but it is easy when you understand what changes can do when you change the settings.
Good luck!

I have both square and circular filters but I use almost always circular ones.
Although I have nothing against square filters you can choose which kind you want to use, circular is my preference because 80% of my lenses take 77mm filter.
However, I strongly advise you NOT even consider Variable Density filters. You will have problems with them especially when you go towards the darker side. Here, I strongly recommend Fixed Density Filters; you may start with a 6 stop and then you decide to get a 3 stop or 9 or 10 stop filter.

APS is a good place for all Nikon repairs. I have been using them for about 10 years now and I am very happy with them. I go to their place, when I visit Chicago a couple of times a year, and drop off my cameras or lenses and they mail them to your home because some repairs take a few days or weeks to be done. They also will clean the camera sensor while waiting and that takes about 90 minutes. They are very reputable and like to walk in their place without having to pack and mail cameras and lenses.

Throw it away and get B & W filters. I had 4-5 Hoya CPL filters that came apart and it was getting too expensive replacing them over and over. 25 years ago I switched to B & W and I have at least 30 B & W filters, mostly CPLs, and none of them has ever gone bad or separated. I learned the hard way and now I know. I have been a photographer for just about 50 years now. Quality may be a little more expensive in the beginning but it lasts. You will forget the extra money you spend in the beginning very soon but the cheap filter breakdowns will stay with you for very long time.

19