If you are going to replace them with boards running in the same direction, then you'd need to cut both sides back to the next nearest joist, and cut them off in the middle so there would be room to screw the new boards onto them. Or you'll need to put new joists in at the point you want to cut them off.

Another alternative would be to just put a few perpendicular boards in the area you've outlined. This would probably look better. To do that you'd need to add some framing to the structure so there would be sufficient wood to nail them to.

Can you get under the deck?

If so you could screw two 2x4 or 2x6's to each side of the existing joist where the boards meet. That will give approx. 7" of total width to work with.

Then remove all of the screws or nails and set your saw to cut a fraction of the depth of the existing decking.

Measure back 2 or 3" from the center line (where the boards meet) and use a chalk line to mark two parallel lines in the same direction you have the red lines now.

Cut the deck boards and remove them. You will then have a "valley" 4 or 6 inches wide the full length (width) of the deck.

Lay in and screw down a 4 or 6 " wide deck board to fill the void.

This will do two things for you.

#1. It will save you a lot of time and money from having buy enough deck boards to cut and ripping some to piece together to match the uneven width of boards that you have now. You will only need two to four 2x"s to screw to the joist and one or two deck boards depending on the width of the deck.

And #2. It will break up the uneven width of your boards as they are now.