I had someone else report that but I can't reproduce it on 1.19.4 or 1.20.1 using only HiveChecker, the plugin doesn't delete or spawn in Bees it just simply tells the server to remove the current Bees from the hive, Spigot/Bukkit handles the rest. It's simply just calling
https://hub.spigotmc.org/javadocs/bukkit/org/bukkit/block/EntityBlockStorage.html#releaseEntities(). It might be a Spigot API bug or another plugin causing issues.
I'd love to fix it and give me something to do but if I can't reproduce nor anyone giving me information outside of a "fix it" then I can't actually fix it.
EDIT: Seems to be a PurPur issue which HiveChecker doesn't support.