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Hello,
when I delete messages from iMessage on my phone, they still appear on my MacBook and I have to delete them manually again.
Everything is sync and set correctly, I guess. New conversations and messages sync normally, only the delete ones still appear on my Mac.
Thanks
MacBook Air 13", macOS 10.15
As per the article https://support.apple.com/en-in/guide/messages/icht1035/mac
Delete a conversation: Select a conversation, then choose File > Delete Conversation. Or, if you have a trackpad or a Magic Mouse, you can also swipe left with two fingers on the conversation in the sidebar, then click Delete.
If you use Messages in iCloud, deleting a conversation on your Mac deletes it from all your devices where Messages in iCloud is turned on.
So check out the messages box is turned as on in an iPhone see the article https://support.apple.com/en-in/guide/iphone/iph3d039b67/ios
Go to Settings 
> [your name] > iCloud, then turn on Messages (if it’s not already turned on).
Read this also https://support.apple.com/en-in/HT208532
As per the article https://support.apple.com/en-in/guide/messages/icht1035/mac
Delete a conversation: Select a conversation, then choose File > Delete Conversation. Or, if you have a trackpad or a Magic Mouse, you can also swipe left with two fingers on the conversation in the sidebar, then click Delete.
If you use Messages in iCloud, deleting a conversation on your Mac deletes it from all your devices where Messages in iCloud is turned on.
So check out the messages box is turned as on in an iPhone see the article https://support.apple.com/en-in/guide/iphone/iph3d039b67/ios
Go to Settings > [your name] > iCloud, then turn on Messages (if it’s not already turned on).
Read this also https://support.apple.com/en-in/HT208532
iMessage sync across devices
