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THREDDS keeps references to netcdf files in cache to speed up the access to previously opened netcdf files. 

The downside of this approach that these files are locked for change as long as they are in the THREDDS cache.

Some processes in the Open Archive like the Archive amalgamate, Copy data and the Merge edited data change existing netcdf files in the archive.

To prevent that these processes fail because of a file lock it is important the disable the caching of file references in THREDDS.

This can be done by the following procedure.

Go to the threddsConfig.xml file and change the following content

  <NetcdfFileCache>
    <minFiles>0</minFiles>
    <maxFiles>100</maxFiles>
    <scour>10 min</scour>
  </NetcdfFileCache>

to the following

<RandomAccessFile>
  <maxFiles>0</maxFiles>
</RandomAccessFile>
  <NetcdfFileCache>
    <minFiles>0</minFiles>
    <maxFiles>0</maxFiles>
    <scour>0 min</scour>
  </NetcdfFileCache>