always best to put in your own mission sub first and build your mission around it. if you want to utilize an existing mission it shouldnt be a problem, I dont know what would have happened in your case you simply load the mission and zoom in on the location of the battle and edit away in situ check for warnings and errors under mission / validate mission in the top bar , warnings are not the same as errors, warnings you can save past but errors you can not. but its just a matter of being careful I think.MM
ps in my own case I save missions to C:\Program Files\Ubisoft\SilentHunterIII\data\SingleMissions\ English
[edit] most here have mission building experience and a willingness to help but there are those who specialize in mission building they
hang out on this thread.
http://www.subsim.com/radioroom/forumdisplay.php?f=198
Mission building tips and FAQ's here
http://www.subsim.com/radioroom/showthread.php?t=93886