You’d think they would be listed under brave://settings/handlers – however I’m also unable to see where a user can view previously allowed protocol handlers and remove them.
Chrome appears to be the same, so I don’t think this is a Brave specific issue, but rather a poor original design by Google.
They should really do what Microsoft have done and implement an area such as edge://settings/content/applicationLinks where users can view and delete them.
Try the following:
1) Go to brave://settings/clearBrowserData
2) Select the “Advanced” tab.
3) Untick all of the boxes.
4) Tick the “Hosted app data” box – so it’s the only one selected.
5) Click the “Clear Data” button.
If that doesn’t work, try the following:
1) Go to brave://settings/clearBrowserData
2) Select the “Advanced” tab.
3) Untick all of the boxes.
4) Tick the “Cookies and other site data” box – so it’s the only one selected.
5) Click the “Clear Data” button. 
Be aware that this will log you out of all websites.