import netCDF4
import numpy as np

nc = netCDF4.Dataset('geo_em.d02.nc', 'a')

lat = nc.variables['XLAT_M'][0,:,:]
lon = nc.variables['XLONG_M'][0,:,:]

lu = nc.variables['LU_INDEX']

newlu = np.zeros( np.shape(lat) )

shp = np.shape(lat)
for y in range(shp[0]):
  for x in range(shp[1]):
    curvalue = lu[0,y,x]
    print x, y, curvalue, lat[y,x], lon[y,x]
    newvalue = curvalue if curvalue != 2 else 50
    newlu[y,x] = newvalue

lu[0,:,:] = newlu

nc.close()