Exiting SSH sessions suddenly killing Apache

Okay, this is a doozy. I'm running Apache 2.4 on Ubuntu 16.04 server instances. I use near-identical environments for both production and testing instances, as well as a near-identical VirtualBox instance that I manage using Vagrant for development. For the longest time, I've been able to SSH into any of these server instances as the same user that Apache runs under, deploy some application code changes, and then run exit to terminate the SSH session, and Apache would be running just fine afterward. Now, however, I can't do an exit without the Apache service encountering a fatal error:

[mpm_prefork:emerg] [pid 23466] (43)Identifier removed: AH00144: couldn't grab the accept mutex
[core:alert] [pid 17750] AH00050: Child 23466 returned a Fatal error... Apache is exiting!

Notes:

• The Apache user is app.
• If I SSH as app, switch to root, restart the service as root, switch back to app, then terminate the session, it kills Apache.
• If I SSH as root, restart the service, then terminate the session, Apache is fine.
• If I SSH as root, restart the service, switch to app, switch back to root, then terminate the session, Apache is fine.
• If I SSH as root, restart the service, terminate the session, SSH again as app, then terminate the session again, it kills Apache.
• Prior to this week, I've been able to consistently SSH as app, switch to root, restart the service as root, and terminate the session without killing Apache.
• I've tried modifying /lib/systemd/system/apache2.service.d/apache2-systemd.conf and changing the line RemainAfterExit=no to RemainAfterExit=yes, performed a systemctl daemon-reload, and finally a service apache2 restart with no effect.

Is there some explanation for the sudden change in behavior? Is there a reasonable fix to restore previous behavior? If not, then what would be best practice for deploying changes to application code and giving permissions for Apache (the app user) to read it without needing to log in to an SSH session as root? The entire reason for logging in as app was to limit the need to log in as root in the first place.

I'm at a complete loss here and don't understand how everything could suddenly be broken.

The root cause of this is a change in how systemd (from 219) handles IPC objects created by logged in users. By default it will remove any IPC objects left after the user logs out. This applies to all non-system users (uid >= 1000). System users (uid < 1000) are not affected.

Since you have changed Apache to run under a non-system user, whenever you log out of that user account, systemd nukes all of Apache's IPC objects, and Apache then complains about losing its mutex and dies.

You can change this behavior by setting RemoveIPC=no in /etc/systemd/logind.conf (the default on Ubuntu is yes) and restarting systemd-logind.service.

It's better to leave Apache running as a system user (e.g. www-data on Ubuntu), and use permissions and ACLs to give www-data access to files it needs to read/write.