In typical Persian fonts which are True Type, there is a historical problem with yeh and kafs, since these fonts are created for Windows 98, which didn't include full Persian support, and now, we have 2 kind of Kafs: Keheh(0x6a9, ک), and Arabic Kaf(0x643, ك), and 2 kind of Yehs: Farsi Yeh(0x6cc, ی), and Arabic Yeh(0x64a, ي). Old fonts use Arabic ones, but the standard keyboard for Persian uses the Persian ones of course, is it possible to edit and fix these fonts? I've made many attempts to replace these characters with FontLab Studio, which I failed. Any suggestions?
@Parsa, two versions of Kaf and Yeh exist because two versions are defined by the unicode standard.
This character is discussed here:
The fact that Farsi and Arabic share a character set but have different variant characters within them is an accident of history which you will have to live with. Sorry!