freebsd-update: handle directories changing to files

Further to f6d37c9ca13f ("freebsd-update: handle file -> directory on
upgrade"), handle the reverse case of a directory changing to a file.
We may not encounter this case on upgradess (before freebsd-update is
retired) but it is needed to support rollback.

PR: 273950
Reviewed by: dim
Sponsored by: The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D41945