When a directory with a full run is copied to a new directory, the links remain, so that the new directory has links which point to the old directory. For some cases this is fine, but some thing need updating. In particular, the link to the input file, i.e.,
Common/InVane -> input_file
is not updated. Thus changes in the input file are not reflected in the intermediate input files. A quick fix is to replace links for the input file only, but there may be other files that are links which should be updated. This same problem would occur if you wanted to run in the same directory, but with an input file with a different name.
When a directory with a full run is copied to a new directory, the links remain, so that the new directory has links which point to the old directory. For some cases this is fine, but some thing need updating. In particular, the link to the input file, i.e., Common/InVane -> input_file is not updated. Thus changes in the input file are not reflected in the intermediate input files. A quick fix is to replace links for the input file only, but there may be other files that are links which should be updated. This same problem would occur if you wanted to run in the same directory, but with an input file with a different name.