OK...
So your publish proceedure only allows you to create a new folder that has all the files in it...
Simply copy your missing file into the new subfolder...
I suppose you tried that...

Tell me... are you doing this work with all your files located in the 3dgs "Work" folder or do you have a seperate folder located elsewhere?
Sometimes all your files need to be in the "Work" folder otherwise the publish process screws up...

When you publish... do you get any error pop-ups?

Try this maybe...
Go into the 3dgs folder and change the "Work" folder name then create a new "Work" folder...
Then copy all your files into the new folder...
Then try publishing...