On import-upstream, unapplying checked-in .pc/ quilt patch-state makes unversioned conflicts

$bzr plugins
builddeb 2.7.0dev
  bzr-builddeb - manage packages in a Bazaar branch.

$dpkg -l
bzr-builddeb 2.8.4

cmiller@hypatia:~/work/canonical/libv8/libv8$ bzr st

cmiller@hypatia:~/work/canonical/libv8/libv8$ bzr ls .pc
.pc/.quilt_patches
.pc/.quilt_series
.pc/.version
.pc/0008_mksnapshot_stdout.patch/
.pc/0011_use_system_gyp.patch/
.pc/0014_disable_cross_build.patch/
.pc/applied-patches
.pc/issue9316131_5001.diff/
.pc/r11654.patch/
.pc/r12161.patch/
.pc/r12336.patch/
.pc/r12460.patch/

cmiller@hypatia:~/work/canonical/libv8/libv8$ quilt applied
0008_mksnapshot_stdout.patch
0011_use_system_gyp.patch
0014_disable_cross_build.patch
issue9316131_5001.diff
r11654.patch
r12161.patch
r12336.patch
r12460.patch

cmiller@hypatia:~/work/canonical/libv8/libv8$ bzr st

cmiller@hypatia:~/work/canonical/libv8/libv8$ bzr merge-upstream --version 3.16.14.11 ../libv8_3.16.14.11.orig.tar.xz
Using distribution unstable
Using version string 3.16.14.11.
Unapplying quilt patches to prevent spurious conflicts
Conflict adding id to test/mjsunit/new-function.js. Unversioned existing file test/mjsunit/new-function.js.
Conflict adding id to test/mjsunit/regress/regress-145201.js. Unversioned existing file test/mjsunit/regress/regress-145201.js.
Conflict adding id to test/mjsunit/regress/regress-2291.js. Unversioned existing file test/mjsunit/regress/regress-2291.js.
Conflict adding id to test/mjsunit/regress/regress-crbug-126414.js. Unversioned existing file test/mjsunit/regress/regress-crbug-126414.js.
4 conflicts encountered.
The new upstream version has been imported.
You should now resolve the conflicts, review the changes, and then commit.

cmiller@hypatia:~/work/canonical/libv8/libv8$ bzr ls test/mjsunit/new-function.js
bzr: ERROR: [Errno 20] Not a directory: '/home/cmiller/work/canonical/libv8/libv8/test/mjsunit/new-function.js'

cmiller@hypatia:~/work/canonical/libv8/libv8$ ls !$
ls test/mjsunit/new-function.js
test/mjsunit/new-function.js