@ Xnyle
If you're trying to preserve the disk, then don't rewrite it until it develops errors, and of course first confirm the error by trying at least two other working drives first.
As soon as you write over the disk with your (uncalibrated) floppy drive, it will not be exactly the same as when leaving the duplication plant or whatever, so it would be the last resort in my mind.
The last last resort incase the disk is u/s would be to split open the diskette case and replace the actual disk inside. This preserves the diskette case and label, so there is nothing to worry about really.
To demagnetise a tape or disk requires a powerful alternating magnetic field, so there's nothing to worry about there either. Just look after them the best you can, you can do no more.