Thanks for following up on this.
It's this scratch on the glass, right:
If so, I suspect it's cause by a piece of sand/grit that was stuck to a print and then fed through the scanner, scratching the glass in the process.
You might be able to get a replacement piece of glass from a broken scanner that you use for parts. Frankly, I suspect the odds of finding a similar replacement scanner in working order might be even easier and not necessarily more expensive.
As a last resort, you could try and contact a company that cuts custom-sized pieces of glass and see if they can make a replacement. However, I consider this a last resort since the original glass most likely has an optical coating and using plain glass without such a coating will likely result in reduced contrast and perhaps flare artefacts. It may also be challenging to fit a replacement piece of glass in the scanner, depending on how it's mounted.
Sorry to not be of too much help other than acknowledging the problem!
PS: one more last-resort measure would be to try and fill the scratch with something like India ink and see if that improves matters. It may cut down the stray reflections that the scratch causes, making it less apparent in the scans.
