Except you're wrong. When you flash a rom it does not overwrite all files found on your phone. By running a master clear, you can clear out all system files and flash back to stock which will generate new files.
However, it is not necessary to run a master clear for all roms to be flashed. For example, I went from cognition to Paragon without running a master clear and its been a fantastic experience thus far. So, if you didnt run a master clear, your phone still retains its battery file and may take a while to learn its averages. Running a clear battery stats can help your phone learn faster.
To explain this further, take a look at a statistically normal distribution (bell shaped curve). Over time, your phone learns what 100% to 0% is an all in between. Well, over a long enough timeline, your battery starts to get closer to the average which means it will start to say that 98% is a full charge and continue to decline. Its just what happens with batteries. If you clear out this timeline, you start to generate new means. This will not restore the life of your battery but it will give your phone the ability to be more accurate about its current state.