You didn't tell what version of OS and SCANDISK, but some did have an option to attempt recovery of bad sectors. BUT a simple format should have it start over.
And SPINRITE definitely does this.
They were put there by scandisk a long time ago after the heads got jerked around, but now that I have them aligned better and its working well they are still there even though I've run scandisk again. Does scandisk scan sectors previously marked bad to confirm their condition when you do a surface scan? I'm wondering if it put them there just because it couldnt read the disk due to bad head alignment and I'd like to remove them and do a new scan to see if I can recover some space.