This is a UAT-driven workflow in the editor that's not currently looking at the INI setting to infer whether or not -nativizeAssets should be implicitly added to the BuildCookRun command line. It should probably behave the same as File->Package Project, which does implicitly add it if the value of the INI setting is not set to "Disabled."

Steps to Reproduce
  1. Launch QAGame editor.
  2. Open Project Settings and change "Blueprint Nativization Method" to either "Inclusive" or "Exclusive."
  3. Choose File->Cook Content for Windows. Note that Blueprint assets do not get converted. Also note the following log output:
BuildCookRun.DoBuildCookRun: WARNING: Project is configured for Blueprint nativization, but the conversion flag (-nativizeAssets) was omitted from the command line. No nativized assets have been built as a result.

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ComponentUE - Gameplay - Blueprint
Affects Versions4.154.164.17
Target Fix4.18
Fix Commit3664561
Release Commit3664561
CreatedSep 9, 2017
ResolvedSep 26, 2017
UpdatedApr 27, 2018