"To reiterate what a couple of people have also said, I would guess (or at least hope) that this update won't negatively affect people's option files. The update will obviously be some sort of downloadable patch which changes some of the game's DEFAULT data. Your option file would only come into effect AFTER the default data, if that makes sense - basically your edited option file should affect the update, not the other way round. I'll try and explain a couple of examples:
If on your option file, you leave Berbatov at Tottenham then you're not changing the default data. So when the update comes out with transfers etc, they'll have moved Berbatov to Man Utd in the default data, so he'll be there in game. If, however, you've already transferred him to Man Utd in your option file then that will supercede whatever's in the update anyway - hope that makes sense.
If we think about the 4 new licensed Spanish teams it gets a bit more tricky. What if on your option file you've already edited the name, emblem and kits for these teams? Well I think that in the update, by default obviously these teams will then have licensed badge and kits and this will overwrite and 'lock out' the editing you've done on those teams. The edited data will probably still be in your option file but the data in the update will make these teams licensed and 'locked'.
There's also a potential issue with created players. The update may contain new players so for example in your option file if you create Gudjohnsen in the created players section then transfer him to Barca, when the update comes out Konami may have themselves created and registered Gudjohnsen into their default data, meaning that when you load your option file you have 2 Gudjohnsens! For this reason I'd suggest not creating any new players until the update. "
