Remove/ Undo Ignore Thread on deleted email
So, luckily, in my case the message hadn't been deleted, only hidden.
There's an option to choose whether or not you want to see ignored threads. Select the folder (in my case, the Inbox), then go to View > Threads > Ignore Threads
This will show all threads you have chosen to ignore. To undo this, select the message you have placed the ignore on, then go to Message > Ignore Thread. Refresh the folder, and all following emails will appear.