If there are Random Generated Groups (RGG) in a file (the square "yellow" icons), you should use the "Save RND Layer...". If there are "regular" units (the square "red" icons), then you'd use the "Save Scripted Layer...". What those two methods of "Save" do is to save only the units that pertain to those types, and leave out any changes you may have made, accidentally or purposefully to the other types. If you have a file with both, then you need to "Save Normal Mission...", else you'll lose one or the other types completely from the file. In all cases, the SH4MissionEditor will make TSR files that you then can delete, if working with Campaign files - though it is not necessary.
If you are making edits to a mod in which lurker_hlb3 made the campaign, such as a version of RSRDC or OM, then after you make edits, there will be automatic changes made to the files by the SH4MissionEditor that will ruin the timing of Lurker's RGG in that particular file. What you should do, if editing his campaign files, is work from a back-up copy, then compare your edits to his original file, using a text editor (or
WinMerge), paying particular attention to the lines "DelayMin=xx" and "DelayMinInterv=", which are often set back to their "default..." values. Other (4 to 5 other) lines are often added that are unnecessary. If you read one of lurker's ReadMe files, he mentions "reverse engineering" his files, and this is why. SH4MissionEditor wants things a certain way, and especially with RGG, they will end up being over 24 hours late after you use the SH4MissionEditor on a file, sometimes not generating at all. Like I say, work from a copy, and compare afterwards...