I would like to know why pulumi deleted resources of my project without any message or permission?

when you run

pulumi up

it would show a preview of the actions it would do before you confirm the changes to be applied on AWS. it looks like a change in your application code might have caused the resources to get deleted. but as mentioned before, this would show up, unless you are running something like

pulumi up -y

or

pulumi up -f -y

to automatically approve with skipping preview.