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WA uses an encrypted form of communication to send chat/app updates. This has been implemented mostly and you can send the following updates:
If you mess up one of your updates, WA can log you out of all your devices and you’ll have to log in again.

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Archive a Chat

To archive a chat, you need to provide the last message in that chat: 
const lastMsgInChat = await getLastMessageInChat(jid) // implement this on your end
await sock.chatModify({ archive: true, lastMessages: [lastMsgInChat] }, jid)

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Mute/Unmute a Chat

You can mute a chat for specific durations or unmute it completely.

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Supported Times

TimeMilliseconds
Removenull
8h86,400,000
7d604,800,000

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Examples

// mute for 8 hours
await sock.chatModify({ mute: 8 * 60 * 60 * 1000 }, jid)

// unmute
await sock.chatModify({ mute: null }, jid)

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Mark a Chat Read/Unread

You can mark entire chats as read or unread by providing the last message: 
const lastMsgInChat = await getLastMessageInChat(jid) // implement this on your end
// mark it unread
await sock.chatModify({ markRead: false, lastMessages: [lastMsgInChat] }, jid)
To mark as read, use markRead: true

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Delete a Message for Me

Delete specific messages from your chat history: 
await sock.chatModify(
    {
        clear: {
            messages: [
                {
                    id: 'ATWYHDNNWU81732J',
                    fromMe: true,
                    timestamp: '1654823909'
                }
            ]
        }
    },
    jid
)

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Delete a Chat

Completely delete a chat conversation: 
const lastMsgInChat = await getLastMessageInChat(jid) // implement this on your end
await sock.chatModify({
        delete: true,
        lastMessages: [
            {
                key: lastMsgInChat.key,
                messageTimestamp: lastMsgInChat.messageTimestamp
            }
        ]
    },
    jid
)

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Pin/Unpin a Chat

Pin important chats to the top of your chat list: 
await sock.chatModify({
        pin: true // or `false` to unpin
    },
    jid
)

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Star/Unstar a Message

Mark messages as starred for easy reference: 
await sock.chatModify({
        star: {
            messages: [
                {
                    id: 'messageID',
                    fromMe: true // or `false`
                }
            ],
            star: true // true: Star Message; false: Unstar Message
        }
    },
    jid
)
The chatModify function is defined in src/Socket/chats.ts:899 and uses app state patches to sync changes across devices.