Usually in cases like this you have to replace the area with the stain. Hopefully you have some extra of this vinyl somewhere - either left over sitting in your basement (ideal) or in some inconspicuous spot like under the fridge, dishwasher or in a closet. You then basically cut the bad section out and cut a piece of the extra EXACTLY the same size and use the special two part epoxy seam adhesive to glue the whole mess down. I have seen this done very well. THere will always be seams but sometimes these can be hidden by cutting them along parts of the printed pattern. I'm not positive how best to insure how to EXACTLY match the exact shape on the replacement piece, maybe a template. Maybe others will chime in on this.