I just had a Brazilian cherry floor put in thru out my house and when choosing it my wife wanted to have double lined borders in a very light wood. It looks really nice the issue is we are having to reconfigure the house; putting up some new walls to add an office and bedroom and will now have it looking weird... borders running under walls.. only on three walls per room etc etc etc..

Could I have the lines stained for it do blend into the rest of the floor? or do I need to have the entire floor stained (which mean I lose the natural look of the Brazilian cherry?

I'd like to attache an image but cant seem to figure our how to.

You may be able to paint the floor the color you want. Stretch tape pressing it down so the lines will not bleed, two rows of tape for each board. After the paint is dry, coat with a varnish to protect the paint from wear.

hi,

staining the lines to match wont work?

You may not get the color to match without sanding to bare wood, although some stains may get close to the right color you will need to treat the floor so the color will be intense enough.
With the extra time that was spent putting in borders, I would spend the time to cut the flooring to complete the design with the right material if it was my house.
The borders hi-lite the shape of the room so helping the design either by coloring in the border or going back to the correct installation should be done, instead of having the border go missing at one wall.