I think you could go over it carefully with a marker, but I wouldn't. We already had one unexpected thing happen while trying to deal with another thing... I'd also be concerned about the soundness of the threads/quilt in general and would treat it delicately, but I'd probably go over with a new round of thread rather than mark each stitch.
As for the black thread, Sewingpup, what I've been told is that black thread is often thread that failed their color tests or had other problems and has been reworked multiple times. So maybe it started as beige and turned into pink and then into black, each time going through sets of processes to set/release color and wind/rewind the thread. Cotton thread, like fibers, do have directions -- many of us have been trained to thread our needles as it comes off the spool. But if it kinks and causes problems, then thread by the cut end so the thread is reversed.