You can use DSCC to perform this task. For information, see Directory Service Control Center Interface and the DSCC online help.
Set the suffix to read-only, as described in Setting Referrals and Making a Suffix Read-Only.
Export the entire suffix to an LDIF file, as described in Backing Up to LDIF.
Import the same LDIF file to reinitialize the suffix, as described in Importing Data From an LDIF File.
During the initialization, the suffix is unavailable. When the initialization is complete, all configured indexes are ready to be used.
Make the suffix writable again, as described in Setting Referrals and Making a Suffix Read-Only.