In future. You should always mention both the compiler and story format, and their versions—because, yes, it's important. Generally, you do that via tags—though it doesn't hurt to also mention them in the body of your question.
In this case, it seems like you're using some version of Harlowe with, I'm guessing, some version of Twine 2.
First. Your example has too many closing parenthesis on the $eatk assignment. I don't know if that was a transcription mistake in the example here or if that's in your actual code, but you might want to check on that.
The (if:) macro, and its siblings (else-if:) and (else:), require a hook after the macro tag. For example:
(if: $amulet is 1)[(set: $mana to 200)]
In your case, it looks like you'll probably want to pair it with an (else:) macro since you have two conditions. For example:
(if: $amulet is 1)[(set: $mana to 200)]
(else:)[(set: $mana to 100)]
With that, the whole thing together might look something like the following:
(link: "Fight Baal")[
(set: $ehp to 2000)
(set: $mhp to 2000)
(set: $ename to "Baal")
(set: $turn to "you")
(set: $hp to 1000)
(if: $amulet is 1)[(set: $mana to 200)]
(else:)[(set: $mana to 100)]
(set: $eatk to 85)
(set: $eatkname to "Slash")
(goto: "Baalcombat")
]