Confirmed. Looking at this when they renamed the part to include the pitch there's a typo so instead of it referencing Pin_Headers.3dshapes/Pin_Header_Straight_1x02.wrl it looks to Pin_Headers.3dshapes/Pin_Header_Straight_1x02_Pitch2.54mm.wrl which doesn't exist.
I just pulled up a design that includes it (JP1 centre near top of the PCB) and from the project the pin header is visible...
Until I changed the footprint to stop using the cached one, and imported the same one you're using there:
And it vanishes.
Might be worth reporting it on the github? I don't see it listed yet, but worth reconfirming my search before adding your report https://github.com/KiCad/kicad-library/issues