In archaic Persian they used to pronounce the word "خواهر", khwahar. But today we pronounce it Khahar, Maybe in the next 1000 years they would pronounce it something else.
If you ask why we say barun instead of baran is like to ask we don't pronounce khahar, khwahar any more. The answer is that every language changes. Khahar is still written خواهر but is not pronounced khwahar. It is the same for barun and baran.
Every one speaks a language but yet there are many illiterate people in the world who can not write, and it used to be much more in for example 1000 years ago; that's why the pronunciation of words changes faster than their writing form.
Yes, the writing form of words also changes, though it takes more time; for example mogh. قبلاً مغو بوده بعداً شده مغ.
About Khwahar I'm rather sure; I've asked a famous Persian language teacher. You might know him, Mr. Seyed Mousavi.