Thank you for your post.
First of all, there is no documentation available for FileMaker Server error codes because most of the error codes can be confusing and misleading. There are a few documented in Knowledge Base Articles.
The error message "some files or folders could not be deleted" is pretty straight-forward, and the usual cause is a file (or files) does not have full read/write privileges. If a folder or file is set to Read Only, then FileMaker Server cannot remove it. Check the privileges for all files in that folder and make sure they are set to Read & Write.