While playing on 1.14.2 on a server running PaperMC (I have also tested this in spigot and in vanilla with the same results, so it is a vanilla minecraft issue), I killed some villagers with `/kill @e[type=minecraft:villager]` while they where sleeping. Later on, when I tried to sleep in the same bed a villager was in when he was killed, it still says the bed is occupied until I break and replace the bed.
Cannot reproduce in 1.16-pre2. Is this still an issue for you?