Hypersmurf said:
A scroll of Empowered Fireball is a scroll of the Fireball spell, modified by a metamagic feat. It is not a scroll of a new spell that is not Fireball. The Save DC of the spell will be 14, not 17.
That's true - but that's not exactly what's happening here. Here, the caster is scribing it in his spellbook as a 4th level spell, or, if he's a sorcerer, learning it as a spell known as a 4th level spell. He's paying the costs as if it were a 4th level spell, and has none of the flexibility advantages of a 3rd level metamagiced spell. At that point, the question is: is this a spell with a metamagic feat applied - even though you don't know the feat, and certainly aren't applying it actively? Alternatively, is this a new spell through spell research?
Judging by the large number of similar spells whose power differs according to level, it's entirely reasonable to take a spell, make it more powerful, and raise the level. That's what I would consider here, although in general, you probably don't want to follow strictly meta-magic guidelines.
Both options make sense, and you'd choose depending on the situation. A question to ask yourself is, for instance: can the "new" spell be enhanced by the fiery spell metamagic feat? If it can, it looks like a real new spell, if it cannot, it looks like a metamagically enhanced fireball. (Of course certain metamagics - like quicken - are inherently unstackable, yet there are still a multitude of swift spells that are true "new" spells). It all depends on the campaign and the circumstances. If a wizard just found a scroll of empowered fireball, I'd let him scribe fireball but not empowered fireball in his spellbook. If it's an NPC using weird magix, and the DM happens to do that using metamagic, perhaps the new spell approach is more fun.