If you block someone and that user clears the history of their secret chat with you, only their part of the history will be deleted.
Due to how Secret Chats work, the Telegram servers don't know what your sending: messages or service commands. After you block someone, Telegram prevents any communication between you and won't know that the incoming message is a
'clear history' action.
Note: In 1-on-1 cloud chats, the other party is able to delete history for both sides because for cloud chats, the server knows that what is being sent is the 'clear history' action.