There doesn't seem to be a way to batch together operations that involve walking through directories and symlinks to do something to a file. This seems to be a major source of complexity.
begin_transaction ();
lstat ("/path", ...);
lstat ("/path/foo", ...);
commit ();
It could also solve the whole thing with ending up with zero-length files because you didn't use the right incantation to update a file atomically on ext4 (https://thunk.org/tytso/blog/2009/03/12/delayed-allocation-a...).