question

With how you have structured the tables, using the row and column numbers as indexes in the "GISPoints" array doesn't make sense. When row and column number are the same you are connecting a point to itself.

You need to translate the row/column header into the correct array index (which is equal to the row where the header appears in the "Locations" table).

if (routes[i][j] == 1) {
                 
            string rowHeader = routes.getRowHeader(i);
            string colHeader = routes.getColHeader(j);
           
            int indexRow = points.getRowByKey(rowHeader, 1);
            int indexCol = points.getRowByKey(colHeader, 1);
            contextdragconnection (GISPoints[indexRow], GISPoints[indexCol], "A");
        }