It may be that you’ll have to look at the first row of eyelets in the dec section and start the next eyelet row so that the eyelets shift correctly. It seems that a shift of 2 sts should do it so that the pattern staggers rather than stacks the eyelets.
ETA: Finally had a chance to try this on needles. You’ve probably worked this out already but just in case, I added one more knit stitch before the repeat in B, row 7. That seems to stagger the eyelets at the join of rows 1-5 of A. Keep repeating the corrected row 7 and the k3tog decreases will take care of the eyelet pattern. The end of row 7 will be k1 or whatever works next to the dec from from 6.
Row 7: K1, yo, k3tog, k2, *k2, yo, k2tog; rep from * to last 2 sts, k1