I thought I'd reply to this even thought it's years later as I spent hours researching this topic with a ton of conflicting answers.
I had a player on IR who went from OUT to QUESTIONABLE. I proposed a trade with another team for a straight 1:1 swap - my WR for his QB. Yahoo allowed the trade to process, we had the "waiting period", last night it posted as successful and the players were traded. So it does in fact allow this to happen. Just to try things out, I attempted to pick up a player off of the wire and it flagged the move as having an ineligible player in the IR spot and wouldn't let me proceed.
So in summary, the 1:1 trade will successfully work with an ineligible player in the IR spot but a waiver move will not.