Sorry, it's not a skip option. Line Select 2 would have been RESTART NAV, which will bring you back to the same page unless you remove the disk.
I don't understand how the FMS would have started the update unless Line Select 1 (BEGIN UPDATE) was pushed. Maybe a case of "That button didn't work, lets try the other one?"
If the navdata in the disk became current in between your flights, that might explain why the unit chose this particular time to display the update page but to my knowledge the page will be displayed any time a card or disk is loaded.
Call Honeywell, let us know what they say.