Re: Reparing netCDF files

>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.