I think if you're climbing really big trees, like Davey Dog and the British Columbia guys, two fliplines is almost essential, long ones at that. If you're climbing 'normal' big trees, the extra flipline is just that- extra.
Let's say you've got a climbing line, towing a rigging line and you've got two fliplines and you're trying to work your way around the crown, a chainsaw hanging amidst all that. Not saying that's a bad situation or anything, it just is what it is. It all depends what kind of work you're doing.
Coming down a spar, we use a flipline as our tie-in once and our climbing line fashioned as a flipline for our tie-in twice, which is two fliplines. A 'second' flipline, in that case would be a third. You could use two fliplines and hip your climbing line, but if for some reason you had to bail quickly, your climbing line is not set and ready.
As far as a flipline too short, generally speaking, your flipline is plenty long for most practical purposes. If, say, you're working down a fat spar and you've maxxed out your flipline, you can attach a loop runner or some other rated sling to extend the length for those infrequent times when you might need it.
The extra flipline, we can assume, is for added safety or versatility, but if you're tripping around in your own kit and things are getting tangled and you're not using one of the items but with minor occasion, you can always change. To really know if it will work for you is to just try it.
I had all kinds of ideas of what it was. 
