all_flags.pb: Properly handle intermediate files am: 4ba41f0e

Original change: https://googleplex-android-review.googlesource.com/c/platform/build/soong/+/27562191



Change-Id: I2649c9dfc715a353ffd74a5988bc7165028547d2
Signed-off-by: Automerger Merge Worker <android-build-automerger-merge-worker@system.gserviceaccount.com>