Yes, the m2v file contains the original CC. If you want to change it with an external program and remux with MuxMan you will have to add it back to the m2v with a program like
McPoodles CC_Mux Other programs accept SCC format. srt is NOT a CC format, but a subpicture format.
Converting CC to srt format is used to change CC to subpictures (aka subtitles) which do not require a display device capable of decoding CC. If this is your objective, MuxMan accepts SST (which uses accompanying bmp files), sup, or sp files.