awk     'function isort( A, B, n,    i, j, holdA, holdB)
                {for( i = 2 ; i <= n ; i++)
                        {holdA = A[j = i]; holdB = B[j]
                         while ( A[j-1] > holdA )
                                { j-- ; A[j+1] = A[j]; B[j+1] = B[j] }
                         A[j] = holdA; B[j] = holdB
                        }
                }

                {N=(NF-1)/2
                 for (i=1; i<=N; i++) {X[i]=$(i*2+1); Y[i]=$(i*2)}
                 isort (X, Y, N)
                 printf "%s ", $1
                 for (j=1; j<=N; j++) printf "%s %s ", Y[j], X[j]
                 printf "\n"
                }
        ' file
ID1 ref_C 5 ref_A 10 ref_B 30 
ID2 ref_H 5 ref_G 12 ref_F 69