After you beat the Elite Four and get the National Dex (so you can see all of the pokemon, not just the ones in the D/P world), you can go to a place called the Pal Park. I think once per day, you can upload 6 of your pokemon from R/S/E/FR/LG to your DS game and try to re-catch them in this park. (I wouldn't worry about losing anything, though: the pokeballs in this park have 100% success rate.) After you catch the pokemon you uploaded, they rate you on your performance (how fast you caught them, etc) and give you berries based on it. Once you transfer pokemon to the DS though, you CAN NOT transfer them back to the GBA games. As for the limit per day thing, I can't think of any good reason as to why that'd be there.
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