Pupils created with BC 1.3+ (i.e. including BC 1.4) are stored in table 'brutes2' and not anymore in table 'brutes'.
This can be a non trivial task due to new BC MD5 encryption and depending on what you would like to do.
For the sake of simplicity, I would suggest instead to export all your brutes directly from Brutal Combo (from the BC menu), then download all masters and IDs using the MyBrute List Manager. At this stage is becomes rather straightforward to keep/deletes the brutes. Finally you can reimport what you'd like to have in a blank BC database (using Squirrel, SQLWorkbench, or the modified BC version by Banane).