Using relative paths within the advanced processing dialog is not an intended feature. It works because the common dialog for opening files (the file selection dialog when loading that CSV file) happens to set the processes' working directory as a side effect of selecting a file.

The program does not keep track of where hash entries come from, other than the path field itself (what is displayed). The program is expecting operations that add new entries to return absolute paths. Even when the buffer is associated with a file, these operations return absolute paths, but the program subsequently corrects these paths, unless it is configured otherwise.

The only real fix for this is to have the advanced processing dialog substitute the directory that contains the CSV file for . in the paths before handing it off to the directory recursion code. This way, if the buffer hasn't been associated with a hash file, you get absolute paths in the result, and if it is associated with a hash file, with the default configuration, those paths will get corrected so that they're relative to the hash file automatically.