Hi KEvans,
Based on the situation, please test as below to help us to narrow down the problem:
1. Test on another computer
2. Try to open these files in windows explorer
3. Create some files and then delete them, see if they still appear in the windows explorer
In addition, please check permissions of these folders. If you have no permissions on these folders, you cannot see them in team site.
To edit permissions for a list, library, or individual item, please refer to the link below:
office.microsoft.com/.../edit-permissions-for-a-list-library-or-individual-item-HA102833689.aspx
Thanks,
Nancy Xie