Do you get a different message for the remaining folders of files? Perhaps it reports the files are bad?
Search the forum for discussions about the "Removed" and "Bad" databases in MC. You can create a Smartlist or View to see what is in them.
If the files aren't bad, but have just been deleted before and now you want to import them again, use a Smartlist/View of the Removed database to find the record of the deletion, and remove that record. MC should then import the files again, as it no longer knows that they had previously been deleted.
I have a Smartlist called "Removed Database contents", but I'm not sure if I created that one, or if it comes supplied with MC by default. Look for it.
Note: If you delete something from the "Removed" database, refresh the Smartlist/View and check that they are gone. There are some circumstances where they can be re-added to the database by MC background tasks, and need to be deleted a second time.
If MC believes the files are Bad, remove them from the Bad database and MC will re-evaluate their condition.
Note for audio files there is an existing Smartlist called "Audio -- Bad Audio files" that you might be able to use as is, or to work out how to create a Smartlist or View to check for other media types.