The first step to re-index the data file is to make a copy of the structure file. Open the duplicated structure file with a new data file. Remove all relations and then go into each table, drop all indices, and close the database. Re-launch the duplicated structure file with the original data file and then close the database. You will now have a non-indexed data file. Launch your original structure file with the original data file. By doing this, 4D will re-index your data file.