There is the separate "Notefix" utility, which you get from Microsoft.
I have the version for GP 9.0 - which, due to its "standalone" nature may work on other versions of GP.
The documentation for it says:
"Note Maintenance
Purpose:
The Note Maintenance utility (NoteFix.Dic) will search all non-temp tables that have a field called Note Index and either rebuild them to the next note index or will search all existing note indices and set the Note Index in the company master to the highest note value. It can also be used to find all the objects that have the same note index and then the user can assign the note to the actual document it belongs to and re-index the rest of the records.
Installation:
To install the NoteFix.cnk, place the file in the local dynamics directory, launch dynamics, and install new code. You can access the Note Maintenance window by choosing File-Maintenance- NoteFix. Choose that to open it. Alternately, you can add the Note Maintenance to the shortcut bar.
Under SQL, a number of tables must be created before using this product. Logging as “sa” or “dynsa” to the company will create them automatically. No further action is required by the user.
Usage:
After opening the Note Maintenance window, the 4 choices are:
Set Note Index to largest note index:
This option will insert all the tables in the list and search them for the highest assigned note index. It will then set the Note Index in the Company Master to that value. This would solve the problem (from here) of having duplicate notes in the system. This is the first maintenance that should be done before any other types are done. Otherwise, rebuilding the notes could possibly cause more duplicate notes. There is also an option to open an expansion window to reset the Next Note to a larger value. This should be used if any 3rd party products use our note table. This is critical because this WILL cause problems in the 3rd party notes if it isn’t reset to a higher-than-used number!
Only Rebuild Notes with Index 0:
This option is normally only needed for records that have been imported with ODBC,IU, DTS, etc. When a record is imported, it is recommended that the note index be left to 0 to avoid duplicate notes. Unfortunately, as of release 4.0, the system doesn’t address adding new notes to existing transaction records very well and it will create a note with index 0. Since everything imported without a note index, they will all have the same note.
Rebuild All Note Indices with Next Note Index:
This option will only be used if the notes for a company are terribly scrambled and you would like to start over. First, delete or rename the Record Notes Master (SY03900). The notes in there would not be accessible after the rebuild and would just take up space in the system. Next, we would need to find the highest note index in the system. Run the ‘Set Note Index to largest note index’. Finally run the ‘Rebuild All Note Indices with Next Note Index.’
Check for Duplicate Notes in Selected Tables
This option will search all the selected tables for duplicate Note Indices. If any are found, another window will be brought up showing the duplicate note and the records & tables it was found in. The window will show a Key (usually key #1) and the Key fields. Using the Dynamics Table Descriptions, you can determine which record that the note is duplicated. The note is displayed to help make this determination. Mark the Keep? checkbox for the record that the note belongs to. Use the browse buttons to scroll through all the duplicate notes.
After all duplicate notes have been examined; hit the Process Button to change the Note Index of all unmarked records.
The Note can be removed in this window as well if you want to. There are buttons allowing Quick Select/Deselect All of the items in the window."
Alternatively, if you can provide a bit more detail on the type of records where you have the problem, I may have useful scripts or other information that I have accumulated over the years.