(This should be for 2.9.1 - this version was not yet available under "affects versions" when filing this bug).

After updating from 2.9 to 2.9.1, most of my settings were overwritten by their default values.

• public signup got enabled
• the language changed back to english (instead of german)
• e-mail addresses were visible again (instead of masked)
• captchas where disabled
• the welcome message was lost
• the site title and url where changed back to the defaults
• daily backups were still enabled, but now including the attachments (which I had excluded)
• etc

Almost all the settings that I had changed using the web interface were changed. However, I noted that the SMTP server settings were still ok, as were the installed plugins and the user macros.
Also, the settings I had copied (confluence-init.properties and atlassian-user.xml) were fine, too.

other settings where still ok

• SMTP server

Just in case this matters, I am using LDAP authentication against an active directory (using atlassian-user.xml).