If anyone should ever run into this problem, they can manually change the conf/maintenance.html to a different name. My host did this for me.

Notes for site administrators:

If you're ever stuck in maintenance mode and want to get OUT of it,
rename the /conf/maintenance.html file to /conf/_maintenance.html .

In order to put b2evolution into maintenance mode, rename this file to maintenance.html (with NO _ at the beginning).

In order to put b2evolution into maintenance mode but still allow access to the install script,
rename this file to imaintenance.html (with an i at the beginning).

Edit the contents of this file to change the message that is displayed during maintenance.

Moved to FAQ

I was doing an upgrade from V5.0.7 to V5.0.8 but the website returns System upgrade is in progress. I have tried the above maintenance.html file solution to no avail. Is there another setting that I can visit or a database setting change needed to regain site access.

I also re-loaded the back-up database but still get the system upgrade notice.

Check for other variants of the maintenance file such as umaintenance.html:
http://b2evolution.net/man/installation-upgrade/configuration-files/maintenance-html