I believe the valley dying is allowing the green leaves in the top left of the screen to run all the way out. Every time you die, the game takes life from the valley to respawn you. The leaves are the valleys life meter. When you spawn be sure to bring as many trees, vines, and animals to life as you can to raise the valley's life. The only times I died was in water from messing up jumps, be sure to always keep an eye on your energy (life) as you use it and take damage, as it deteriorates from the same meter causing it to drop quickly in some amita and dark encounters. You can die 4 or 5 times before the valley dies.
If you get into some serious trouble inside of the soma facility or reactor and need to regenerate the valley, you can use the travel option to travel back to the beginning of the area, or into different areas. This will lose any checkpoints in the area, but can get you out of a tough spot if you really need it. This shouldn't be too much of a challenge playing normally as long as you keep up on energy upgrades and L.E.A.F upgrades.