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.
Also Telegram is open source, so you can't be sure when you ask Telegram to clear history that it's actually doing so. For example in my own custom version of Telegram, when someone requests to clear history, it sends me a notification that they made the request, then tells the server the history was deleted, but it doesn't actually delete the history on my side. Another workaround some people use is to run TelegramCLI on a shell and have it output chat logs to to a syslog daemon where they can be archived on the client side. You can then run a report that diffs the TelegramCLI logs against the syslog archive and tells you who is deleting chats on you.
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