Yes, using MKVMerge. Go on and use MakeMKV to first pull in the 1 huge file so you can work with it.
How: #1 download mkvmerge (
http://www.bunkus.org/videotools/mkvtoo ... loads.html)
(assuming windows, I believe its the same on mac but just in case I'm wrong...)
#2 Launch MKVGui (unless you're a command line ninja)
Load up the file in input
#3 Load up the same file again in the chapter editor
#4 Using any media player find the cut points between the episodes. (it doesn't have to be exact, just close enough). Cross reference these numbers with the exact chapter editor timings.
#5 Under the global tab, "Enable Splitting" then "after timecodes" and paste in each time code from the chapter editor you want split at.
Example: 0:27:35, 0:55:10, 1:22:45
#6 At the bottom give it an output name...it'll will affix -001 after each file.
#7 Hit "start mux" or if you're doing several "add to job queue" and you can have it split them apart.
Notes:
From my experiance it generally only takes slightly longer than the time it would take to copy the file.
Ignore the warning it gives you about the chapters from the chapter editor not being loaded...we only did that to get exact timings....not to re-insert new chapter points. (Already existing chapter points will carry over to the split files)
Enjoy
Tolken