music deleted from the "automatically add to iTunes" folder

Songs in this particular folder are relocated by iTunes according to their metadata. It is quite normal for them to be removed from this folder and re-filed according to their artist/album. Are you saying that you can't locate the native files now? You can go into Song Info in iTunes and under the File tab you'll see where iTunes put them.

For the "Apple Music" files you're referring to, if these are downloads from your Apple Music plan you may have to re-download them if you moved them while your Mac was being serviced, could be part of the "protected" status of such files.

Content you place in the Automatically Add to iTunes folder should be added to the library and moved from that folder according to the metadata, e.g. artist and album folders for music. In other words the default state of the folder is empty if iTunes is running. If you copy one folder on top of another on a Mac the original version of the folder is replaced with the new one, the content isn't merged. Without knowing more I would suspect this is what you have done. Apple Music content can be transferred from one computer to another if you migrate the library as a unit (see Move your iTunes library to a new computer - Apple Community) but you cannot import the files into a different library. The Apple Music files you have will need to be deleted and then you'll have to make fresh downloads of them.

tt2