Hey,

While the plugin is working fine, that actually may be the problem. I'm not sure if this can be avoided, but it should be noted that worlds that were created prior to 1.13 will regenerate existing chunks as if they were new. This causes MagicLoot to generate structures into chunks that existed before, destroying any builds that were there.

I've temporarily removed this plugin; the only solution from my end is to explore my world until I've found all my existing structures, but this is quite time consuming.