I am not sure if I am reading this right, but if you 'reset' the menus so they point to the programs on the mint9 install then the programs on the mint6 install won't work (one of the downsides of a separate /home partition I guess, but peculiar to Fluxbox since very few DE's or WM's use the /home folder to locate their menu files). I guess you would have to have one menu with entries for both the Mint6 and Mint9 programs, but it might look a bit crowded !
Anyway, if you decide to do this then you need to know the following. The main menu is in the file ~/.fluxbox/menu which is a plain text file editable in any text editor, whilst the sub menus are in ~/.mint-fm2/submenus again plain text and easily editable. So you could manually add the Mint9 entries to the Mint6 menus or alternatively you could extract those two files from the live cd copy them to your home partition and then add the Mint6 entries to them.
Lastly you could always forget about Mint 6 altogether and have Mint 9 and something newer on the old Mint 6 partition - that is what I would do!
Fujitsu Lifebook AH532. Intel i5 processor, 6Gb ram, Intel HD3000 graphics, Intel Audio/wifi. Realtek RTL8111/8168B Ethernet.Lubuntu 13.10,Ubuntu12.10 (Unity), Mint16 (Cinnamon), Manjaro (Xfce).