Reproduction steps:
1. Open project attached (APIrepro.zip) with Unity 5.6.

Expected result: API Updater will show up.
Actual result: API Updater does not appear.

Note: There was a fix in 5.6.2p1 and API updater should be launched in this situation. A link to issue tracker: https://issuetracker.unity3d.com/issues/dll-breaks-after-upgrading-to-5-dot-6-and-up

The project was upgraded from 5.5.3p3.
API Updater shows up on later versions like 2017.1 and 2017.2 but it does not mean that this problem would not appear on these versions as well.

Workaround: Reimport assets to force API Updater.

Regression is not checked.