Documents already uploaded can be deleted from a submission, but only while the submission is in "draft" status, i.e. it has not been sent to EMA yet. Additionally, the whole submission can be deleted when in "draft" status, including all uploaded documents, allowing an applicant to restart from scratch.
Once an application has been submitted to EMA, it is only possible to request a withdrawal, but not to delete the submission, or to remove any files uploaded, even if the submission is reopened for an update. This is by design and there are no plans to change this in the future.