I've been working with a client who needs to put a file containing thousands of images on FMGo for the iPad. The first file was a bit under 8GB, and iTunes was able to move it onto the iPad. Then the client decided they wanted higher resolution images, and the file size went above 10GB. iTunes would attempt to move that file on, but it failed repeatedly. Sometimes it said the file had been moved, but the moved file size was smaller, between 9 and 10 GB. I looked at moving a smaller file and then having it import data from a server to get its full record set, but that took over an hour. Since multiple iPads needed to be loaded on a weekly basis, it wasn't a practical option.
I ended up splitting the file into two > 5GB files, and iTunes was able to move those over without a problem. Retrofitting the main file so that image display calculations conditionally used one file or the other was a pain in the backside to implement, but otherwise it worked.
To me, the larger point is that despite what FMGo is capable of running, iTunes and/or iOS itself may be the limiting factor in the size of files that can be deployed to iOS.
BTW, I investigated using Air Sharing to move the files on, but that app can't access the folder where FMGo files are stored.