Highlight "Flare" and enable it but don't throw it. When it is low, press Left or Right and highlight another object.
Then, highlight "Flare" again. It will have restarted and you will not lose another one.
Skip the Second Boss:
When standing in the warehouse just outside from where the second Thing boss lurks, have
an ally to stand near the garage door to the left of
the Boss' door,
then back up and throw a grenade at them. If done right, you can cause the character to run towards the
door and it will open. Run inside before it closes.
Thanks to Revolution readers Thedrid and DJ!