Gear ratios and dynotuning?

I wanted to build up the 9" I got for my car with 3.50 gears, but because I'm going to be taking a 2 month trip to Europe this summer, I don't have the funds to build it for this summer.

I wanted to know if I could dynotune my car with the 2.80 gears and put the 3.50 gears in later, or will my tune get messed up when I change my gears?

Thanks!