Explanation on practice. If you try to save your object, e.g.:
Set<Folder> folders = message.getFolders();
folders.remove(inputFolder);
folders.add(trashFolder);
message.setFiles(folders);
MESSAGESDAO.getMessageDAO().save(message);
you don't need to set updated object to a parent object:
message.setFiles(folders);
Simple save your parent object like:
Set<Folder> folders = message.getFolders();
folders.remove(inputFolder);
folders.add(trashFolder);
// Not set updated object here
MESSAGESDAO.getMessageDAO().save(message);