The “use custom path” checkbox in the import manager of the editor has mysteriously disappeared, causing all maps to load incorrectly in the editor, and can no longer be saved using any custom assets. This happened spontaneously and with no changes to any files or maps.
EDIT: So, apparently the “use custom path” checkbox is no long part of the editor. However, I did receive some sort of bug that broke all imported files. However, re-importing everything fixes the problem, despite being incredible time consuming.