I changed the size of a pen for ease of access and, thinking it was my only option, overwrote the preset.

Is this irreversible? The image has also gone.

Linux
$HOME/.local/share/krita/paintoppresets
Windows
user\Appdata\Roaming\krita\ or %APPDATA%\Roaming\krita\paintoppresets
OSX
~/Library/Application Support/Krita/paintoppresets

Just move the brush presets in here on a backup folder and restart.

bwall, sorry for the hurried response today. Here is a link to the documentation page on how "Loading and Saving Brushes" (in case):
https://docs.krita.org/Loading_and_Saving_Brushes

bwall wrote:Is this irreversible? The image has also gone.

No, it's not irreversible. Within the folder "painttopresets" you should see a file named as the brush you've overwritten, just remove it out from the "painttopresets" folder, then close and restart Krita, and the brush with the default settings will be restored (along with it's icon).