Haven't found the code in question, but here's an example:

Build: https://luci-milo.appspot.com/buildbot/chromium.fyi/ios-simulator/5129
Failure: https://luci-logdog.appspot.com/v/?s=chromium%2Fbb%2Fchromium.fyi%2Fios-simulator%2F5129%2F%2B%2Frecipes%2Fsteps%2Fisolate%2F0%2Fsteps%2Farchive%2F0%2Fstdout

16:29:09.648644 Unable to walk "/b/rr/tmpY8DGeE/w/src/out/Debug-iphonesimulator/sql_unittests.app": walk("/b/rr/tmpY8DGeE/w/src/out/Debug-iphonesimulator/sql_unittests.app"): lstat /b/rr/tmpY8DGeE/w/src/out/Debug-iphonesimulator/sql_unittests.app: no such file or directory

Compile Step: https://luci-logdog.appspot.com/v/?s=chromium%2Fbb%2Fchromium.fyi%2Fios-simulator%2F5129%2F%2B%2Frecipes%2Fsteps%2Fcompile%2F0%2Fstdout

Isolate example:
- stdout: https://luci-logdog.appspot.com/v/?s=chromium%2Fbb%2Fchromium.fyi%2Fios-simulator%2F5129%2F%2B%2Frecipes%2Fsteps%2Fisolate%2F0%2Fsteps%2Fgenerate_45.isolate.gen.json%2F0%2Fstdout
- gen.json: https://luci-logdog.appspot.com/v/?s=chromium%2Fbb%2Fchromium.fyi%2Fios-simulator%2F5129%2F%2B%2Frecipes%2Fsteps%2Fisolate%2F0%2Fsteps%2Fgenerate_45.isolate.gen.json%2F0%2Flogs%2F45.isolate.gen.json%2F0

According to compile, the file was generated here:
... in dir /b/c/builder/ios_simulator/src/out/Debug-iphonesimulator
    /sql_unittests.app/Info.plist

However, isolate is looking for it at: /b/rr/tmpY8DGeE/w/src/out/Debug-iphonesimulator/sql_unittests.app

We need to update the isolate code to look for files relative to the actual build output directory rather than relative to the start directory.