In the designer for the last form, if you go to the variables tab and add the variable for the file uploads onto the form, when the process runs it will include the current data for the variable.

For example, if you upload 2 files in the first form and the last form includes the same variable, then it will show those same 2 files. If you added 2 files in step 1, but removed 1 in step 2, then it would show 1 file on the last form, and so on.

You can only include files in a save to repository task if the variable(s) are included on the form, however, if you don't want the users to see or interact with them, you can make it read only on that last form or use field rules to hide the variable entirely.