Whenever you load a world, the advancements found in its "data/advancements" folder are loaded, overwriting whatever custom advancements the server already maintains. Effectively, advancements from the most recently loaded world are used, instead of the default world.

Steps to reproduce:

• Start server with custom advancements in the "world/data/advancements" folder.
• Via some plugin, load an additional (normal) world with an empty "data/advancements" folder.
• Notice that all advancements have been wiped.

With many other global data (player data, maps, etc), Spigot uses the contents of the default world's appropriate sub-folders. Only advancements show this behavior. Therefore, I suggest that advancements should only be loaded from the default world.