That is very odd.
If you want to restore the surface color, I would be inclined to try a paint or a dye. The dyes are probably easier to apply - kind of wipe on and wipe off (different for different products). I think the Cerakote stuff qualifies as a dye. The paint will be more work because of a little more cleaning prep, masking and what may be a two step process if the particular paint you use needs an adhesion promoter.
I have no direct experience with using dyes on rubber; but, I expect that the paints may be more long term durable than the dyes. Because paints are an actual coating they will probably do a better job of protecting the rubber and may last longer. The down side is if you screw up a paint job (runs , dust motes) it will definitely be harder to fix than a botched dye job.
There are a bunch of flexible surface paints on the market. Some available at corner auto supply stores and some form more 'specialty' suppliers. I have use Colorbond on flexible plastic like surfaces with excellent results (repeat restoration of the front lip). It sprays on with multiple thin coatings and ends up with an excellent surface if you do it right. Thing is, it is listed for leather, vinyl and flexible plastics and rubberized plastic (whatever that is). Rubber is not in the application guide and I expect that most of those flexible surface paints do not include rubber in their application guides. However, I don't know whether the boot part of the sash is truly rubber or a really flexible plastic of some kind. The boot does seem to have a very smooth and almost shiny surface to it so it might actually be one of those plastic like products.
Perhaps try a dye first, just because it will be easier. If the results are not good, then move on to a paint. However, I would be inclined to go to an auto paint supplier or an auto body shop to see if they will provide you with suggestions for a product. I had a '71 car on which I did a resto and the back bumper had a rubber strip on it which was looking pretty scabby. The guy who did the paint work used a paint product to restore the strip and 10 years later it is still looking good so the products are out there, you just need to find them.
As a final note, I have replaced the rear sashes on my car because of torn boots (badly adjusted windows). Removing and replacing the sashes is a lot of work and can potentially screw up the glass adjustment. You will likely need replacement retention clips (never in stock at Acura) for the lock rod because I think the chances of getting those clips off without breaking them is probably less than 10%. If you are going to paint, assess whether you can paint without removing the sash from the door.
. Attached is an example stock photo that looks similar to my issue. Is there a way to restore the rubber trim's black color back to it's natural state?
