Joel,
Just received a 300 f2.8 lens. It had a large 122mm UV filter on the front, but no filter installed in the 39mm holder in the lens. I had thought that the 39mm filter was necessary for proper focus, but in researching, I get conflicting opinions.
Thom Hogan is a widely respected authority on Nikon. In his review of the Nikon 200mm f/2 and 400mm f/2.8 he states:
As with all Nikon drop-in filters, the supplied plain filter is part of the optical formula; using a filter holder without glass is a slight no-no.
In his review of the 300mm f/2.8 he states:
Filters are the special 39mm drop-in variety. You get two drop-in brackets with the lens, and if you're not using filters, the one with the flat glass element in it should always be used (it's part of the optical formula).
In summary, for optimum performance you should use a Neutral Clear (NC) that would have been included with the lens originally (I think the part number is 2478NASI), or a C-PL1S polariser filter available separately for the 300mm f/2.8. Instructions for Nikon drop in polariser filters is attached for your information.
Also, the holder can go in both ways so not sure which way is correct.
I have attached a photo showing the C-PL3L drop in polariser for the 200mm f/2, left, and the NC that was included with the lens originally, right.
You can see "front" marked on the polariser (refer also to attached pdf of instructions) and also how the filter is closer to one side of the holder than it is to the other. Hence, an NC should be inserted into the lens such that it is closer to the front lens element ("front") than it is to the lens mount ("rear").
I assume that it goes in with the filter screwed in from the front like a regular filter on the outside of the lens.
In the case of an NC, no (refer to attached photo). In the case of a polariser, it is irrelevant because the filter is integral with the holder - if you purchase a drop in polariser the product you will receive is the filter
built into an accompanying holder (due to the rotating wheel mechanism) - you swap filter and holder as one when inserting/removing a polariser drop in filter.