Hi @SamStig ,
Ensure you have set up a macro folder. To do this, in Alteryx, go to Options->User Settings->Edit User Settings:
...then select the "Macros" tab.
Hit the button.
Navigate to the folder you would like to use for your macros.
When you have done this, open the .yxmc files in Alteryx. You will get a warning if you're using an old version of Alteryx but it will be fine to continue. Then simply save it to the macro folder you just set up. You should now be able to see the tools in the "In/Out" section of Alteryx.
Then open the workflow (the .yxmd file). If you see two black boxes with question marks in them, then you need to replace them with these tools. The first is the Dynamic Sheet Names tool, and the second is the Input Multi Schema Flat Files tool. The workflow should look something like this:
On each of the new tools, go to the "Questions" tab and select "Fullpath" from the dropdown.
To remove the sheets you don't want you can place a filter after the first macro, which lists all the sheets it found. You can remove the ones you don't want.
Let me know if this works.