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FYI: in case you haven't seen this, you can now use ncks to apply mapping (ncks -w map_file.nc ...), and benefit from NCO's flawless preservation of metadata & provenance.
When remapping a multi-time file, the time dimension should be preserved as the "record" dimension in the remapped file.
Currently, this can be done with NCO after the fact...
ncks -O --mk_rec_dmn time $OUT_NAME $OUT_NAME
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