So I delete everything in my appdata folder except for wallet.dat and it restarts but now my balance is at zero, all transactions still there but balance shows zero. Have I lost the coins or do I have to wait for the blocks to rehash?
You deleted everything in the AppData/Roaming folder except the wallet.dat file?
Is the client re-downloading the blockchain now?
You might want to let it re-download the entire blockchain, close the client, copy the wallet.dat file to the folder, and then restart the application...
I'm not sure what use the wallet.dat file is without the entire blockchain in place...