Some pictures/images aren't viewable from my daytime office computer (certain protocols & websites are blocked). I finally logged on just to see the work... NICE!!!
Luckily it's lane stitch & if you really want to correct the orange & yellow, it shouldn't be as hard as trying to work around threads that would fill a void in loom or square/box. Lane stitch repair/correction would only affect those lanes (humps) but would need to be carefully considered in order to have enough thread to tie off each side of the portion to be retained. Let your spirit guide you...
I'm assuming the zipper stitch is similar to the edging of rosettes (fret edging)? I've done this with rosettes & used it to edge as well as join the backing onto the piece with all the threads showing by going through both pieces before coming back up through the bead & adding on the next two. This would work great to edge a bag. Some excellent pictures & instructions can be found by any search engine on the internet.
-B- "We do not inherit the Earth from our ancestors, we borrow it from our children."