See Resolving filesync Conflicts. In cases where files on both sides have changed, filesync attempts to determine which version should be chosen. If filesync cannot automatically determine which version should be selected, it prints out a warning message and leaves the two incompatible versions of the file unrecon- ciled. In these cases, you must either resolve the differences manually, or tell filesync how to choose which file should win. You can then re-run filesync to see whether or not any other conflicts remain.
Many users choose to create the packing rules file manually and edit it by hand.
Users do not create or edit the baseline file. It is created automatically by filesync and records the last known state of agreement between all of the files being maintained. Over a period of time, the set of files you want to keep synchronized can change. It is common, for instance, to want to keep files pertaining to only a few active projects on your notebook. If you continue to keep files associated with every project you have ever worked on synchronized, your notebook's disk will fill up with old files.