OK, I had a good go at IFOedit, looks like a powerful tool, but I was lost, and couldn't find any guides to what I was trying to do, then...
I found PGCedit (free from
http://www.videohelp.com/~r0lZ/pgcedit/index.html), and it saved the day.
I was cautious, backed everything up, then opened it up, only to find it automatically backed up my IFO's for me, and had a Macro in the main toolbar which did everything I needed to do, 3 clicks and it was done!
I did need to use muxman (free from here:
http://www.mpucoder.com/Muxman/) to create .ifo, .bup and .vob files for my advert first, but that was easy too.
So if anyone else needs to mess about with their DVD structure and they don't have the Encore file, use PGCedit, it's brilliant.