I have registered a new AMI (instance-store AMI) so I bundled, upload the bundle and registered. So my question is, could I delete this files from S3? or I have to leave this files to get my AMI work for my new intances?
You must leave the image and manifest files in S3 for the AMI to work.
Amazon creates cached copies of the AMI if it is frequently used, so it might not break right away if you clear out S3 and test it, but it will cause problems eventually.
That said, I recommend using EBS boot AMIs instead of S3 based instance-store. EC2 won't even let you delete the EBS snapshot that stores the EBS boot AMI.