We don't modify data of any other plugins and in fact we create our own tables to store our data, so we would not have removed any widgets.
I'd like to help you fix this so here are a few possibilities:
I'd ask your hosting provider to check for table corruption in your database. Installing a new plugin may have triggered a latent issue in your DB.
Immediately check your website error logs. If it's table corruption or something similar, you'll see a ton of messages there.
It could be that the issue is not that your widgets have been removed, but that your website is not reading the DB correctly for some reason e.g. your DB is running out of connections, timing out etc, so the site isn't getting the data it needs to load them.
I'm assuming you've tried disabling our plugin and your widgets are still missing, but in case you didn't, try that.
Also ask your hosting provider to check if your server disk is full, this would also cause an issue like this under certain conditions.
That's about all I've got. Happy to help further even though this is probably not a Wordfence specific issue but more likely caused by a server or DB having problems and installing a new plugin triggered them.