The fix was in
https://github.com/koreader/koreader/pull/7753.
When the download is ready and you click "install" the first thing it does is broadcast a request to save settings (see
https://github.com/koreader/koreader....lua#L485-L498). Maybe the broadcast is not received before the app is killed.
The broadcast itself ought to work, as is the same used to save settings in the rest of scenarios.