I've never used Synteko but, generally speaking, if the scratch is in the finish ONLY, you sand the scratch out, then refinish JUST the area you sanded. You refinish it as you did the floor the 1st time except on a smaller scale. Of course, you'll be doing all the work by hand w/o the need for power tools.
If the scratch is all the way though to the finish, your best bet is to just sand the 'high sides' level w/the rest of the board, then stain the 'white' area ONLY. Stir the can well each time you 'dip' into it. If you want to err on one side, err on the side that's LIGHTER than the surrounding stain. After it's dried for a day or 2, then refinish as I mentioned above.
The only 'catch' is to talk to the Installer about Synteko. I can't specifically advise you on that. My best to ya and hope this helps.