Bungy,
If the bike was not in the run position you would not get the ecm information. What you can do incase the mt6 file got corrupt some how is take and open a new mt6 like the 127LL005.
This is one of the times where you wish you could see what is going on

. If you want to give it another go let me know what happens. Incase your feeling adventurous I have outlined below how copy what you have in the map you are having issues with to a new map.
I am also curious what the exact error is that your getting when your trying to load the file.
Have you ever seen someone tune your bike with the black box you have ? Just to be sure you have the correct black box?
First off rename the file to whatever you would like to call it and then leave it alone.
now go open a 2nd version of the race tuner software. Load the mt6 file that your not able to load now.
next go to the bottom of your screen where the blue bar is and right click with your mouse and tile horizontally or vertically which ever you prefer.
Now your going to have to open the mt6 file that is possibly corrupt first and go to table selection. now with your mouse highlight that entire set of boxes not just the first one but all of them. then go to the pull down menu under the word edit and click on copy with all the files highlighted (shortcut is to use ctrl C for copy and Ctrl V for paste)
Now go to your LL127 map and go to the same menu page in this case Air Fuel is the first one and click on the all the boxes or just the first one and paste from your original file now if you click on only the first one to do the paste you have to be sure that your map has all the same RPM's etc like down to 7500 or 7000 etc ....
Now you have to do this for every single menu page, so make sure as your clicking back and forth that you have the same pages on both instances of your tuning software.
-harry