It sounds like they are lost for good.

Lesson to other people: Remember you need to back your wallet up after every transaction!
(The wallet metaphor is actually a bad one, because it makes problems like this more common than they should be.)
Edit: (more explaination)
When you do a transaction you always spend ALL of the coins in that address, part of the money goes to whoever you're paying, and there rest is returned to you an a new 'change' address. (This helps your anonymity as someone watching cannot tell which amount you spent and which amount you kept.)
Before transaction:
Address1: 9000
Address2: 0
After transaction:
Address1: 0
Address2: 1
Address3: 8999
It sounds like you have wallet.dat that contains the private keys for Address1 and Address2, but not Address3.
(Although the numbers in your story don't add up.)
What were the Bitcoin addresses? (If we know these we can do some more in-depth block chain research)