I perform the same operation all the time, without problems. Capture in SnagIt, save as PNG, import by ref, and then update the graphic.
To fist this, first, I'd save the file out as MIF and reopen it and save it because the fact that you can't import anything would make me suspect that it's corrupted.
There aren't any numeric limitations in FM, but you may be bumping into a RAM, network time, or swap space problem.
Why don't you try saving the single massive (MIF-washed) file out into three or four component parts and see if that helps? Shouldn't make any difference in the book file at all, and it would certainly lessen the load on the system.
Art