If a patch affects an unknown file a and it is qimported, qpushed, and qpoped, a
will be deleted.  Below are the commands to reproduce.

mkdir tmp1
mkdir tmp2

echo hi >> tmp1/foo
echo h2 >> tmp2/foo

diff -uNr tmp1 tmp2 > unified.patch

cd tmp1
hg init
hg qinit
hg qimport ../unified.patch
hg qpush
hg qpop
ls -l foo
#ls: foo: No such file or directory <- bad