A couple of things to supplement what KaleunMarco said:
1. After you open the first file, and click on the "Merge" option for the next file, be certain that the "Mark merged data as saveable" tick box is clear, no checkmark.
2. With that setting, you can then edit the first file's data and "Save" it just fine. Doing this can help you in properly locating groups and ships that you edit, so they don't spawn into other groups and units...