You can have a list of levels (paths) on an array, and load them when needed, for small things it should be fast (or instance+add current, preload the next).
Also, instanced scenes can be changed into "InstancePlaceholder" (check instanced menu) and instance them when needed.
For styles more metroidvania, your "entry/exit points" can have a reference to the next level and load/preload them on ready, once loaded, the instancing+adding is nearly immediate.
If each level is huge, the level structure may need some extra partitioning, like preloading entry points first and doing background loading of the rest while playing, also freeing old level data in chunks.