When you save a map you have been working on using a new name, only the mission.sqm is placed in the "Newmapname" folder it creates.
Simply copy everything else over to this new folder and it will work fine.
Also a debugging tip when creating maps
At the start of every new script you create write the line
titleText["Starting *****.sqs", "Plain Down"]
and at several important intervals throughout.
This is how you find out what line is causing problems in a script that doesnt work
Once you know the script is working okay, either delete the line or place a ; at the start