I don't know if this a Windows codec thing or Avidemux itself. I use the Windows version of Avidemux to join and rotate VR360 videos, when I save to MP4 the 360 Metadata from the source files is lost. I would like an option in the MP4 Muxer to 'inject 360 metadata' (either copied from the source files, or manually added like the "Spatial Media Metadata Injector" free utility I am currently using does).
Avidemux doesn't use any "Windows codecs" and the issue has nothing to do with de- or encoding of video. It is purely demuxer / muxer thing and the question of passing the data structures along the chain.
I'll have a look (spherical projection metadata seems to be supported by libavformat for MOV/MP4 and MKV) when I finally find time for Avidemux again, but indeed, a very niche request.