Firstly you need to undo the joined yarn and neaten off the ends if necessary. Fold the two ends over each other, overlapping by a couple of inches, and then continue with your scarf as if you were knitting with one strand. Once you have completed the next couple of rows the join is camouflaged by the overlaying ruffles.
Or, you can also sew the two ends together with a small overlaying hem.
I also found this great video on Youtube by Paradise Fibers (see button below) showing a similar method of joining in the ends which results in placing the join high within the cavity of the ruffle and therefore doesn't show once the following rows are completed.