Lens Calibration With or Without a Lens Filter?

The general principle would be to set up for lens calibration in the way you would normally use your camera equipment.

If you always or almost always use your lens with a clear protective or UV filter that's how the calibration should be performed.

Having said that, we know filters (even expensive, high quality filters!) can and do degrade optical performance and in rarer cases can make a significant difference to calibration results.

A filter is another glass element placed in front of the lens and often the impact of this extra element will show up as higher than normal astigmatism.

Calibrating with the filter (if that's how you always tend to shoot) will mean any impact of the filter is taken into account and provide a suitable calibration result. However if you see strange results or very high astigmatism try calibrating without the filter to compare and make an informed assessment.