You mean you saved your SH3 folder from C drive?
In that case, I don't know what is going on. Just a question. If you reload your last save file, does it show the emblem you had? If not, maybe the emblem you were using is missing... Were you using an emblem from an separate emblems pack or from the ones in the game?
Try to reload your last save, go to your base, finish your patrol and try to choose an emblem again... if that fails, you will have to wait for some other kaleuns advices.
CapZap