Unless files are not overwritten in the process, or particle doubles aren't added (which doesn't happen often) this shouldn't affect your other maps. You'll tell when a file needs to be overwritten when you see a prompt asking you to replace the file. This is just fine in textures, markings, etc. though. It's usually objects you need to keep an eye on.
And also, .fhs, .fhw, .fho and such files belong in exports. Music files go in sounds.
