U+0259 Latin Small Letter Schwa is only encoded as the byte sequence 0x02,0x59 in the UTF-16BE encoding. It is very unlikely you will be working with byte strings in the UTF-16BE encoding as it's not an ASCII-compatible encoding and almost no-one uses it.
The encoding you want to be working with (the only ASCII-superset encoding to support both Latin Schwa and Cyrillic Schwa, as it supports all Unicode characters) is UTF-8. Ensure your input is in UTF-8 format (if it is coming from form data, serve the page containing the form as UTF-8). Then, in UTF-8, the character U+0259 is represented using the byte sequence 0xC9,0x99.
str_replace("\xC9\x99", "\xD3\x99", $string);
If you make sure to save your .php
file as UTF-8-no-BOM in the text editor, you can skip the escaping and just directly say:
str_replace('ə', 'ә', $string);