1.     create empty target file
       add dimensions and global attributes to target
     
       for each variable in the source file
            add the variable definition to the target file
            copy the variable's attributes to target
            copy the variable's data to the target
     

2.     create empty target file
       add dimensions and global attributes to target
     
       for each variable in the source file
           add the variable definition to the target file
           copy the variable's attributes to target
     
       for each variable in the source file
            copy the variable's data to the target
     

Timings on a 44 MByte WRF model output, with about 100 variables:

Timing for Method 1

Timing for Method 2

NetCDF-4 note:  For netCDF-4 files, schema changes are efficient.

Timing for Method 1 with a netCDF-4 target file

2011 Unidata NetCDF Workshop > Formats and Performance