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Hi, john john Pter. To delete messages sent by members, team owners have to be allowed that via Messaging policy as below.
The "Owners can delete sent messages" is "Off" by default on Global policy. Therefore, to allow that operation to specific team owners, create a custom policy with the setting "On" and assign the policy to the owners.
I have confirmed a team owner assigned the policy with "Owners can delete sent messages" is "On" can delete messages sent by members via Graph API as well. I hope this helps.