If it helps, and it is just one slot, I can create a set of Gerber files for just that one object, that is a plated through slot with a rectangular pad. You'd have to specify the XY coordinates of the two outer drill holes of the slot, the drill diameter, the length and width of the rectangular pad and, of course, the units you are using. It should take only a few minutes.
With the Gerber file viewer, GerbView (and probably many others) you can check the combined results of multiple Gerber layers or drill files for correct alignment etc. That does not mean, though, that your board manufacturer will be prepared to handle multiple files for the same layer. Special attention would needed for the solder masks.
It is also possible to merge Gerber files, at least according to some instructions I found, but it is a not something I would want to go through.