My experiences tell me that young fry do whatever they damn well please, and there isn't an awful lot that you can do to get them to change their mind.
Some of my fry stay at the surface, no matter what. Others hide in the gravel. Some hide in a particular spot on a plant, at a particular depth. Others just turn invisible for a week and taunt me by swiming past when there is no chance I can reach the net in time. Most seem to return to the place they came from if they get disturbed.. whether it be by net, fish, whatever.
I've realized that if they're good enough to hide from me, they'll probably be good enough to hide from the rest of the fish until they're big enough to avoid being eaten. I've caught some bigger ones that have been in the community female tank for over a week and done quite nicely thanks.
Aren't swordtails less likely to eat their young than guppies? I think I remember reading that one of the bigger livebearers (swordtails or mollies) will generally tolerate their fry unless they are particularly hungry. Guppies, on the other hand, will eat anything if it fits in their mouth and tastes good. Regardless of whether they're hungry or not.