When you are in a subdirectory, include resolution just is simply relative to the subdirectory. E.g. we could do:
subdir/index.bigb
= Subdir
\Include[notindex]
\Include[subdir2/notindex]
subdir/notindex.bigb
= Notindex
subdir/subdir2/notindex.bigb
= Notindex
It is not currently possible to include from ancestor directories: github.com/ourbigbook/ourbigbook/issues/214.