The first time an existing chunk from an older world is loaded in 1.13 (by player or plugin), custom block populators that are currently active will be run as though it were a brand new chunk being generated. This causes an unwanted retrogen that can destroy player content. Vanilla populators are not run, only the ones added by plugin. If --forceUpgrade has been used on the world beforehand the problem still occurs.

If a chunk has already been loaded at least once in 1.13, the populators do not fire during future loads of the chunk.

Edit: The world test1 was generated under 1.12.2 with no plugins and has not been converted to 1.13 yet. With a default config, the plugin GiantCaves will generate large caves that can be found at x:250 y:25 z:400 and x:100 y:20 z:700. Both locations are part of the already generated terrain and should not have those caves forming.

The code for GiantCaves can be found here: https://github.com/OtakuMegane/GiantCaves