So the bottom line is that you had a route set up and some of the shops got cancelled. All you can do now is scramble to find fillers and, assuming you can't reschedule all the others, run the route.
It sucks, but your options are few.
Perhaps you will get to redo the ones already done and tainted? Perhaps those were closer in geography to you? Maybe some extra $$ will flow from there.
Don't you wish there were business insurance for this unexpected and unforeseeable loss?
Stuff happens. It's happened to me. I did the shops I contracted for. Didn't come close to break even.
But I have a long memory! Chances of me signing up for more shops for that MSC are slim.
If your relationship has been good and trusting with the MSC, this is annoying but should not destroy your trust or respect. Accidents and oversights happen to all of us. Do scramble for more shops to fill your existing route and cancel the remaining shops for this MSC if you must. Be annoyed, but don't throw the baby out with the bathwater.
Since this is a very long trip you do not want to do twice and they have offered you the choice to cancel the remaining shops with no penalty to you that sounds like a good solution to me. .