When it comes to scratches on double glazed sealed units there are basically three alternatives:
1) Replace the sealed unit. It may seem “over kill” to replace otherwise perfectly good sealed units – but for a lot of people (including double glazing installers), the effort required to polish out scratches is just too much.
If we factor in the time and effort it can take to remove a scratch successfully then this approach will for many have it’s advantages. This said, it is always worthwhile at least trying the other two alternatives below, especially if it is a very minor scratch.
2) The second alternative basically involves filling the scratch in with a resin that has the same refractive index as the glass, so the scratch no longer shows. You could have a look in motor accessory shops, which sometimes sell kits for dealing with windscreen scratches.
3) The third alternative is to polish the scratch out.
This involves a fair amount of effort and of course elbow grease! Do not use any abrasives such as Brasso Duraglit or any kind of abrasive papers of any kind. Window Installers and Double Glazing Repairers most commonly use very fine abrasives such as Ceria (cerium oxide) or Jeweller's rouge (iron oxide). It is important to emphasise that household abrasive cream cleaners are totally unsuitable – they just don’t work and if there is a lot of abrasive in them they will scratch the surrounding glass.