The alchemist's Mutagen class feature says:
At 1st level, an alchemist discovers how to create a mutagen that he can imbibe in order to heighten his physical prowess at the cost of his personality. It takes 1 hour to brew a dose of mutagen, and once brewed, it remains potent until used. An alchemist can only maintain one dose of mutagen at a time—if he brews a second dose, any existing mutagen becomes inert. As with an extract or bomb, a mutagen that is not in an alchemist’s possession becomes inert until an alchemist picks it up again.
A non-alchemist who drinks a mutagen must make a Fortitude save (DC 10 + 1/2 the alchemist’s level + the alchemist’s Intelligence modifier) or become nauseated for 1 hour—a non-alchemist can never gain the benefit of a mutagen, but an alchemist can gain the effects of another alchemist’s mutagen if he drinks it. (Although if the other alchemist creates a different mutagen, the effects of the “stolen” mutagen immediately cease.) The effects of a mutagen do not stack. Whenever an alchemist drinks a mutagen, the effects of any previous mutagen immediately end.
If I'm currently under the effect of a mutagen, and I brew another one, what happens?
Do I lose the effects of the current mutagen, or does it still apply?
The closest thing I can think of is a spellcaster preparing an extended Mage Armor that last for a day or so, and you would keep the effects of it when you prepare another spell in that slot.