[netcdfgroup] How to resolve dimension mismatch between NCEP reanalysis data and rotated lat lon grid

          Here is hoping my question is on topic :-)
I downloaded NCEP reanalysis data from a THREDDS server and my dimensions
are the following - time(record dimension), lat,lon,level

When I do a nf_inq_var it turns out lat and lon are 1D arrays.

I then transformed my global coordinates of NCEP into what is known as
rotated lat lon grid(common in  mesoscale modeling  such as WRF, etc)

 https://github.com/thiasB/unrotMe/blob/master/geo2rot.f90 using the two
subroutines - phi2phirot and rla2rlarot.

I now have the rotated latitude and longitude but these are now  two
dimensional arrays. That is for each global latitude and longitude I have a
rotated latitude. And similarly for a rotated longitude.

How do I write this rotated lat and lon back to the netCDF file given the
fact that dimensions are different ? What I mean by that is I want to
replace the original lat and lon of the geographical system with the
rotated lat and lon of the rotated coordinate system.

I am guessing I will have to create a new netCDF file and copy all the
other information over to that file.
Or is there a way to make the edits to the original file itself ?

Any other alternatives will be deeply appreciated.