The only potential issue I could see would be that the dimensions of the boards might not be the same, so you might not be able to do a one-for-one swap out. So you might have to pull out 4 boards, put down 3 and have a gap. Then pull up 4 more, put down 3 more, etc. And the new boards might be thicker or thinner than the old ones. As long as you're not using the deck to the extent that the gaps or height difference will pose safety hazards, I don't see a problem. The ipe isn't the largest component of any live load the deck joists may be carrying. Humans are. No issue with needing to beef up the joists for wood weight. Use screws, not nails, on the ipe. And pre-drill holes in the decking (not PT below).

Better to figure out where your joints will be & double up the joist. You can of course use a drill & make pilot holes, that will keep the boards from spliting. Al

Yes. If they are rusting now, they are only going to get worse. Use stainless screws.

I just finished redoing my old cedar deck. It had developed surface cracks all over. A few were cracked all the way through and I had to replace those. But for all the rest of the deck I found a product called Elmers oudoor wood filler that was stainable at Lowes Hardware. I had a kid sand and renail those boards and fill the cracks with that product. Then he resanded the filled places and stained the deck. I can tell you it was a ton cheaper than replacing the deck boards (the few I replaced cost me $400 for about 12 boards about 12 feet long in construction heart redwood). The filler doesn't match perfectly but at the age of my deck it looked fine. I used Cabot's Australian Timber Oil in flame mahogany. Everyone comments that it looks great.