Our vector borders allow full modification of geometry. In order to use the modified version of the border, you will need to create a new brush.
To do that:
Your new border brush will be added in the Brushes panel.
1) Make sure you have not turned off, locked or misplaced the bounding box layer of your border tile. It should be beneath all layers, with no fill and no stroke applied.
2) Locking any group of elements of your border tile will make selecting them impossible and they will be left out from the new border brush. And vice versa - locking and turning groups off is an easy way to create new borders with selected elements by your choice.
3) Oftentimes after applying your border brush Illustrator renders it with thin white "gaps" between the border tiles. If they come and go when you zoom in and out, it is only a matter of preview and they will not be present after exporting your work. If the "gaps" persist you need to readjust your border's bounding box and clipping mask.