Perhaps you removed files from local storage using Finder, rather than using the Remove Download option within Music. This would leave Music looking for that local file rather than expecting to stream the track from the cloud. You can use the method below to attempt to fix broken links in the library where you do still have the relevant file. Alternatively you can select tracks in blocks and use the right-click > Remove Download option to clear the links to local files. Tracks that are where they can be found will be removed from local storage. You might want to check the iCloud Status of these tracks first, in particular you should resolve any issues with waiting tracks as these wouldn't be available for streaming and might be deleted if stored locally.
The "missing file" issue with exclamation marks happens if the file is no longer where iTunes or Music expects to find it. Possible causes are that you or some third party tool has moved, renamed or deleted the file, one of its parent folders, the drive it lives on has had a name change, or you've moved a non-portable library to a different path (see Make a split library portable for details). It is also possible that iTunes or Music have changed from expecting the files to be in the pre-iTunes 9 layout to post-iTunes 9 layout, or vice-versa, and so is looking in slightly the wrong place, (see the iTunes Media Organization section of Managing your Mac media libraries - Apple Community for details) or that you've been too aggressive when deleting duplicates at some point.
Select a track with an exclamation mark, use Cmd-I to get Song Info, then click No when asked to try to locate the track. Look on the file tab for the location the library thinks the file should be. Now take a look around your hard drives. Hopefully you can locate the track in question. If a section of your library has simply been moved, a folder renamed, or a drive label has changed, it should be possible to reverse the actions. If the difference between the two paths is an additional Music folder in one path then this is a layout issue. I can explain further if that is the case. If everything is where it is supposed to be try Repair security permissions for iTunes for Mac - Apple Community.
In some cases the library may be able to repair itself if you go through the same steps with Get Info, or when playing a track, but this time click Locate and browse to the lost track. It may then offer to attempt to automatically fix other broken links. Although it says something like "use the same location" I think it expects to find the tracks in the same artist & album layout they were in previously, with one systematic change to the path.
If you want me to try to provide specific advice please post back the following details:
- The location of the media folder under iTunes|Music > Preferences > Advanced
- The location of a sample missing track shown under Song Info > File > Location that begins file://
- The true path to the file whose details you gave in 2
See also FixLinks - an AppleScript to repair broken links in Music - Apple Community.
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