Issue 689531 has been merged into this issue.

The following revision refers to this bug:
  https://chrome-internal.googlesource.com/clank/internal/apps/+/d39c696e3d52629f7491ac73d822b3dcb8c12cc6

commit d39c696e3d52629f7491ac73d822b3dcb8c12cc6
Author: Peter Kotwicz <pkotwicz@google.com>
Date: Tue Mar 07 02:04:44 2017

Repro steps:
1) Enable "Improved Add to Home screen" in chrome://flags
2) Enable --bypass-app-banner-engagement-checks in chrome://flags
3) Navigate the browser to https://tests.peter.sh/notification-generator/
4) Install the web page to the homescreen via the app banner
5) Relaunch Chrome and navigate to https://tests.peter.sh/notification-generator/
6) Try installing the web page to the homescreen via the app banner again.

Expected:
The banner eventually hides
Actual:
The banner never ever hides