You should knit those stitches. The reason is that it brings the working yarn to the tip of the right needle (or now, the end of the stitch holder) so that you're ready to knit the right shoulder sts, the k29 in the instructions below..
"Next row (RS): K45, slip last 16 sts worked onto stitch holder for centre neck, k29
Work right shoulder (as worn) sts only"
Once you've completed this knit row, turn and purl back to the last 3sts, p2tog, p1. The instructions want you to finish this shoulder first. Of course, you can do both shoulders at the same time but the simplest thing may be to follow the directions at least this first time through. It's a very explicit pattern, even giving you the directions for shaping the left shoulder instead of just instructing you to "reverse the shaping". I'd put a sticky note on these rows and move it row by row. You've got the idea and you'll be fine.