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NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
>From time to time during a long run, I close the netCDF files and reopen them later. This of course updates everything, including the unlimited dimension. If you have no other reason to close the file, the ncsync/NCSNC functions (Synchronize an open netCDF file to disk) may interest you. This doesn't repair your existing files, but speaks to your last paragraph regarding prevention of this problem.
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