Run 26" wheels on a 29er I recently bought an 13.5 Trek Cali for my daughter (9 years old).  I got an incredible deal on it and bought it sight unseen from an out of town seller.  After getting it, I realized it had 29" wheels on it instead of the 27.5 the more current models have.  I was actually looking for a 26" at the time, but it was such a great deal, I couldn't pass it up.

I like that it is something she will be able to grow into, but the tires are absolutely huge for her.  I did some modifications (moved some spacers and flipped the stem) so it is definitely ridable.

I am curious if I could throw some older 26" wheels on the bike for the next year or two until she gets more comfortable with the bigger wheels.  It has disc brakes so that shouldn't be an issue.

I know she is going to have a much lower BB that may lead to a few pedal strikes and it is going to look a bit akward with the longer seat tubes and forks.  But since I am changing both wheels, it shouldn't affect the overall geometry too much.

So what do you think?  I know it isn't ideal, but any reason it wouldn't work?

Edit:

I have seen this question, but it addresses only changing the front wheel (which would change geometry.  And also this question about going down to 27.5, but he is looking more for performance improvements.
If you look at bike literature from the early 29er years it was the best thing to buy. There were some issues that showed up after they became common enough for recreational riders. Recommended frame sizes tended to put people on a frame that was actually to large. It seemed that they forgot about the top tube being raised 1 1/2 inches by the larger wheels. Another issue when 29 inch wheels were put on small frame sizes was toes striking the wheels while turning and pedaling. So while a small size 29er may seem odd now they were a one point common. Manufacturers seem to have learned a lesson from all this and now put 26 inch wheels on the smallest frames 27.5 on the less small frames and make larger frames in both 27.5 and 29. All this is just to explain why you have a small frame with 29 inch wheels. The good news is that with the 27.5 boom 26 inch disc wheels are available with steep discounts. I don't see any reason it wouldn't work. It might be cheaper to buy an entire used bike if  you add in tires and tubes. Use the wheels until she out grows them, put the 26's back on the used bike and sell the whole bike for likely close to what you paid for it.