Line 6 Monkey should pick this up for you, but it is definitely listed on the Downloads page, if you select M9 as the product and scroll down below all the versions of Line 6 Monkey that have been released.  The current M9 Flash Memory version is 2.04 and was released on 26 January 2011.

To perform the update, you need to have the latest version of Line 6 Monkey installed.  You need to connect your M9 to your computer using a MIDI Interface (one like the M-Audio Uno is recommended) and then you need to run Line 6 Monkey which should detect your M9.  Monkey will indicate which components need to be updated (if any) and then you simply highlight the item - i.e. Flash Memory and click Update.  Let the update complete fully before disconnecting - it may take around ten minutes.  Job done

See this document which covers it precisely (the version of Line 6 Monkey mentioned is out of date as we're up to version 1.43 now): http://line6.com/support/docs/DOC-1632

Nick