"My Sites" gone after doing clean upload of WordPress files

I found that someone had hacked my site recently, so I was following the list of security protocols to follow. In doing so, I uploaded new WordPress files for all of the following:

• Main directory
• wp-admin directory
• wp-includes directory

I did NOT upload a fresh version of wp-config.php — saved my previous.

Now, none of my MU sites are showing up in the “My Sites” drop-down on the menu bar at the top of the page.

When I go to my Network Admin Dashboard, it DOES show “You have 10 sites”, but there doesn’t appear to be a way to view them from the Network Admin area.

If I go to one of the sites directly, the WP menu bar at the top of the page still allows me to access that site’s Dashboard, however, all the users who should be assigned to that site are completely gone. It’s this way across the MU network.

I attempted the solution in this thread of commenting-out lines 699 and 700 of wp-includes/user.php and that did not solve the problem.