Insert the code below into an agent and make sure to change the "set runtime security level" setting to #3 Allow restricted operations with full administrator rights. (assuming your ID has sufficient rights on the server). Also be sure to add the %INCLUDE "lsxbeerr.lss". The "-F" parameter ensures that just the full-text index is updated, not the views.
%INCLUDE "lsxbeerr.lss"
Sub Initialize
Set session = New NotesSession
Dim db As notesdatabase
Set db = session.currentdatabase
Dim doc As notesdocument
Set doc = session.DocumentContext
Dim consoleReturn As String
consoleReturn = session.SendConsoleCommand(db.server, "load updall DATABASE.NSF -F" )
End Sub