My HD has started making noises associated with bad blocks. Is there anyway to fix this without formatting and re-FTPing?

what kind of noise? if its a detached platter its pretty much a paperweight, got a few of those myself

No it's working fine except in one area where data is stored. I was thinking like a scandisk in my PC or similar to fix it but because of the format I can't see it working.

Some drive manufacturers provide a utility which will scan for and remap bad blocks. Maxtor used to do it. One of my drives developed bad sectors (taking a hammer to the PC does that). Once I scanned it, it would rattle when it got to the dodgy sectors, picking them up from the end of the drive instead. No bad sectors reported, though!

Check the manufacturer's website, download any utilities associated with your drive.
Unfortunately, the drive is likely to get wiped during the process, so you may want to back up your saves first!