The trick is making sure the survivors carry the consequences of the conflicts with them. To keep the physical repercussions from ending the story before it even begins I use one of three things:
Magic, Science, or Time.
- One character is unaffected because of the nature of his magic
- One character is unaffected because he MacGyver's an air-filter and vents the room
- One character suffers vivid, violent hallucinations but is none the worse because of genetics
- Other characters die because they lack the right magic, science failed them, and they're trapped.
The subsequent chapter deals with the repercussions of that moment.
- Those who were physically unharmed, are politically damaged
- The character in throes of hallucinations has to go through detox
- The deaths become consequences with which many people must contend in more than one chapter
Admittedly, in first drafts, I'm not always as good as I ought to be about recovery times. That's what editing and Google are for. Yes, I do search for the approximate real-world recovery times for certain injuries. Sometimes it's not as much as I'd assumed, and other times a significant magical/scientific intervention is needed. Similarly, I also search for complications that might arise from said injury--have to make those darlings suffer!
Fixing a bogus recovery can be as simple as introducing a time delay via a sentence or two. Occasionally, the onus of success in a scene has to shift to a different character because the original character is still injured. Sometimes, the damage has to linger for the rest of the book and become a new challenge for the character...which means enduring the editing aggravation of questioning every subsequent physical action to verify if he/she physically capable of the act. Worst case, the original injury has to be unwritten or lessened.
Of course, the most fun of the SFF genre is to manifest better magic or invent better science! Less fun is going back and seeding said "better" solutions, but seeding is necessary for the recovery to be plausible.
Plausibility is the key injury and recovery.
As long as it's plausible, the readers will keep reading...and your characters can keep getting into increasingly more catastrophic mischief and mayhem.