I went to Riverwood as I got there it came under attack by a dragon Alvor and Sigrid both got killed by it. I then went to Whiterun only to find it under attack by vampires Belethor got killed by one of them. I'm fine with NPC's getting killed but why don't they get replaced by someone new ?. Belethors shop is now permanently closed and Alvors blacksmith shop is empty. I like the random attacks I like NPC's getting killed in them but the Skyrim my character lives in is fast becoming empty.
Bad luck on getting both Alvor and Sigrid killed. I went back to Riverwood and found Alvor had been killed. Bummer, he was useful, annoying. One way around it is to do a reload, that solves it. I don't know how long ago my Alvor got killed, it must have been some way back, and I didn't feel like re-doing all that I had done since then, I'll just have to live with it.
Reload if it happens is the answer.
NPCs do repopulate places that you have cleared though, not as many, but some.