eLindy,
you are correct, that FileSync is intended to adjust the database entries for files and folders, however there seem to be issues in special situations, where this seems not to be working correctly. please check your file names for special characters (like ' ), if found, please correct the name and retry. If there are still issues, please check folders table for duplicate name / path values per portal by entering the following statement inside Host :: SQL
SELECT * FROM {databaseOwner}{objectQualifier}Folders
and do same for files by running the following query:
SELECT * FROM {databaseOwner}{objectQualifier}Files