I can only tell you what I would do if they were mine.
If that will be acceptable, this is what I would do:
1) Remove the laces and take the shoes in my hands. I would feel the leather. This is to test pliability or how easily the leather bends. You don't have to be rough but, for example, bend the tongue of the shoes. See if the shell still has enough of its natural oils and strength. If you sense that it is too brittle, then do not proceed any further.
2) If it is determined that the shell is still tough enough and pliable, I would wet a terrycloth, ring out the water, so make it damp, then apply leather lotion to the shoes and let them sit for an hour. Then wipe off any excess.
3) Then, in a well ventilated area (or better yet, outside in daylight) wearing rubbler gloves (the kind you wash dishes with is fine) Take some Acetone on a DRY terrycloth and swiftly pass over the blackened area. If the dye has not penetrated the shell, it should come off. If the sye HAS penetrated the shell, you can try a second pass with a refreshed application of acetone on a terrycloth.
If the colour of the shell lightens in that area (it may or may not happen on the first pass) then you'll have to do the entire shoe to maintain a consistent colour.
DIsclaimer: Personally, I have never done this on shell but the acetone is your only hope if you can't live with the black marks, then you should be able to get most of it off.
4) The worst that can heppen is that you have lightened the shoes and minimised the black.
The best that can happen is to be completely successful and lose the black marks altogether but still lighten the overall shoe colour.
5) If successful or not, you must get moisture and oils back into the leather. Shell or not, acetone wil WILL remove oils so you need to apply leather lotion or whatever special lotion you would use on shell to prevent cracking. You may have to apply a few times over 24 hours just to make sure.
Again, this is what I would do if they were mine and only if the shell is in good strong condition.
Before starting any project like this one, I would be at the pont of 'do it or I'll never wear them'. This is what gives the courage to experiment in that one is willing to lose the shoes to gain the knowledge. The final choice is yours ofcourse. Personally those black marks would bother me and I would proceed, but that is me being a perfectionist about it.
You may want to contact Nick V or DWF and see what they have to say as they have far more knowledge and hands-on experience with shell.
Be patient and get as much input as possible before deciding what course of action to take.
Hope this helps....if you do proceed and it works, the post photos!