Let me preface the answer with an honest confession. I had heard that riddle and the solution before (but for some reason had to think really hard to figure it out today), and today while trying to figure it out again, I got help from a couple other people on sajha chat.

Divide the coins into two groups. Group 1 has 9 coins, Group 2 has 41 coins
The number of heads in Group 1 : say, "a". The number of heads in group 2: 9-a (because we had nine heads to begin with)
Flip all the coins in Group 1.
You have 9-a heads in Group 1 now.
No. of heads in Group 1 = Number of heads in Group 2 = 9-a.