If the local mail replica where a managed mail replica, then the next time the database is initialized during client startup, it may well compact the database when it detects that there is a large amount of whitespace in the file in question.

If not, then the user will have to run the command manually and it can be tricky depending on where and how you installed the client.  I usually add the location of the Notes executable files in my path, then go to the data folder where the file I want to compact is located.  Then I can run the NCOMPACT -D -C -i [target-file-name].nsf  It will then ask for the password on the ID file of the user identified in the active notes.ini and attempt to compact the file.

All of this will need to be done from a command prompt, maybe with admin rights depending on the security settings in the OS.