Ok, I do this, then when I save the new IFO, it asks me, "Do you want to save it as .BUP aswell?" Well, do I? Thanks!
Yes, ultimately you want to save it as .BUP as well. .BUP file is simply a BackUP of the .IFO and the two should identical.
Of course, it's wise to save copies of the original .IFO's before altering them permanently with IFOEdit. Personally I put copies of the original .IFOs &.BUPs in a seperate folder on the DVD when i burnt it, just in case I need them in the future, e.g. for re-torrenting, etc.