You don't say HOW the pleats are stitched so I will assume they are not top stitched but sewn so the stitches are not visible from the outside

It may be too difficult a task for you to remove the lining and repair the stitching from inside so the best bet is to stitch invisibly from the outside. This is not particularly difficult to do but takes a steady hand, good eyesight and TINY stitches

From the outside, place the point of the needle about a quarter inch inside the pleat and bring the needle point out at the crease, right at the bottom of the fell (the bottom of the pleat). Carefully place the needle into the underlying fabric, keeping the pleat well aligned, and back out again about one eighth of an inch in the direction of the waistband (i.e. upwards), catching the top part of the pleat right at the crease. Re-insert the point of the needle downwards into the underlying fabric and repeat the previous step, moving up 1/8 inch and again catching the creased part of the upper pleat. The result should be invisible but if it is not, rip out the stitches and start again. You do not need to stitch through all the inner layers of canvas and lining, only the outer fabric

Sorry I don't have a picture but one of the other kilt makers may have something available to demonstrate what I mean