The Cambodian language pack has not yet been released for 3.x. It may soon. That lang-tagged flag had a wrong tag as Cambodian is km-KH, not km-KR.
It is safe imho to do this change:
The km_kr.gif is unlikely to have ever been used as this kind of naming is only systematically used at Joomla install time when using the multilanguage installation(new feature in 3.x). No Cambodian pack = no possibility to use it per default.
Otherwise, if someone had used the older 2.5 pack for Cambodian (updated a multilang 2.5.x site for example), the original flag since 1.6 was and still is present (km.gif)
joomla-cms-bot
- 
zero-24
- 
Bakual
-
Code for the language Khmer as per ISO 639-1 is km
Code for the country Cambodia as per ISO 3166 is KH
As per ISO 3166, the code KR that is currently used points to the Republic of Korea - Not Cambodia as needed.
So, the renaming of the flag icon file that represents Khmer language from km_kr.gif to km_kh.gif is correct.