Personally, if it were me, I'd take the test now, and I'd keep a photocopy of it before sending it in.
Presumably what they mean by the two months is that they'll give you two months from the date of the letter -- when they send it -- and, yes, if you don't pass, you'll have to submit a whole new application.
It's a rotten thing that happened to you; but the Home Office are not known for resolving these things with all deliberate haste -- so if I could get myself out of the whole mess by taking another test, then that's what I'd do. The extra cost and time is a hassle; but not as much as waiting God-knows-how-long for your this thing to be straightened out.
Good luck.
Will