When regenerating the the build files, the working directory isn't saved. This means that relative paths in the command line that were correct on initial generation are incorrect on regeneration.
Repro in Chromium:
[scottmg:~/work/cr/src ((0023f0453fc0...))]$ cat x.txt
//base:base_unittests
[scottmg:~/work/cr/src ((0023f0453fc0...))]$ gn gen out/test --runtime-deps-list-file=x.txt
Done. Made 8401 targets from 1466 files in 3706ms
[scottmg:~/work/cr/src ((0023f0453fc0...))]$ touch base/BUILD.gn
[scottmg:~/work/cr/src ((0023f0453fc0...))]$ ninja -C out/test
ninja: Entering directory `out/test'
[0->1/1 ~1] Regenerating ninja files
FAILED: build.ninja
../../buildtools/mac/gn --root=../.. -q --runtime-deps-list-file=x.txt gen .
ERROR File for --runtime-deps-list-file doesn't exist.
The file given was "x.txt"
ninja: error: rebuilding 'build.ninja': subcommand failed
Comment 1 by bugdroid1@chromium.org
, Feb 22 2018