If you start the break in with one fuel of a certain nitro content, it is best if you stick with either the same brand and nitro content...or at the very least finish the break in with the same nitro content. Meaning if you start the break in with 20% nitro, then finish the break in with 20% nitro.
After the break in is complete, you can use whatever you like...but as mentioned, you can expect to have to retune the engine. Your mention of running a couple of tanks of light load on the engine (half throttle) is a good idea and will help the engine adjust to the higher or lower content, but you will still need to retune for performance.