This issue is under discussion here: #1165

It is not desirable for us to have _FillValue = NaN for dimensions and coordinate variables.

In trying to use xarray, _FillValue was carefully kept from these variables and dimensions during the creation of the un-resampled file and then were found to appear during the to_netcdf operation. This happens in spite of mask_and_scale=False is being used with xr.open_dataset

I would hope that downstream code would have trouble with coordinates that don't make logical sense (time or place being NaN, for instance). We would prefer NOT to instantiate coordinate variable data with any fill value. Keeping NaNs out of coordinate variables, dimensions and minima and maxima is part of our QA/QC process to avoid downstream issues.