Sql-server – How to determine what MDF files are in use

When you do "Tasks -> Shrink" from the GUI it actually issues a DBCC SHRINKDATABASE command behind the scenes. Try it. When the dialog box comes up, don't click the "OK" button. Instead, click the "Script" button. You'll see the command in a query window. Combine that with a query on sys.databases (leave out master and msdb), and you can make a script to shrink all of the databases.

For example (taken from jcolebrand's comment):

SELECT 
      'USE [' + d.name + N']' + CHAR(13) + CHAR(10) 
    + 'DBCC SHRINKFILE (N''' + mf.name + N''' , 0, TRUNCATEONLY)' 
    + CHAR(13) + CHAR(10) + CHAR(13) + CHAR(10) 
FROM 
         sys.master_files mf 
    JOIN sys.databases d 
        ON mf.database_id = d.database_id 
WHERE d.database_id > 4;

Copy the output of that query and run it to shrink all your files.

I'm 99% sure that setting a file to offline is a one-way operation. The only route to bring them back online is to restore the data from a full backup and then apply log backups.

There may be an obscure hack route to get this working but I'd be inclined to rebuild the database. Create a new database, transfer the schema you want to keep, copy the data across.