I was waiting awhile to see if anyone would provide an answer to your question about colored Matching Points.

In Panoweaver 5  HELP | help  I did a search on "Matching Points"  then I selected paragraph 6.2.3 Stitch

"When Panoweaver stops stitching to remind you to add matching points, matching points in these images become green, and the mismatching points in these images become red, other points you add are in other colors. The location of each pair of points is shown as coordinates(x, y) and recorded in matching points list in Matching Points Panel."

I would suspect your readjusted matching points  would change colors until rerun, in which case IF PW5 stopped to ask you to fix the matching points again.. those new ones would be green = good  red = NEW mismatched point sets.

Hope this helps