The TLDR is the subject :)
It used to be that the wrapper scripts would apply command-line flags passed to the "run" command, and if none were passed, any existing command-line flags file would be deleted.
This has been surprising to many, so now:
1. To clear flags, use "out/Default/bin/chrome_public_apk run --args="
2. To re-use whichever flags were last used: "out/Default/bin/chrome_public_apk run"