Už je vyřešeno.

Na zrušení diakritiky u všech písmen funguje:

$basename
$search = array("ě","š","č","ř","ž","ý","á","í","é","ó","ú","ů","ď","ť","ň","Ě","Š","Č","Ř","Ž","Ý","Á","Í","É","Ó","Ú","Ů","Ď","Ť","Ň");
$replace = array("e","s","c","r","z","y","a","i","e","o","u","u","d","t","n","E","S","C","R","Z","Y","A","I","E","O","U","U","D","T","N");
$filename = str_replace($search, $replace, $basename);

je to v souboru s utf-8 kódováním, některá písmenka s diakrikou psaná na klávesnici jsou jiná než ta která jsou vidět v názvech souborů v exploreru

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Na ponechání diakritiky i u souborů uložených na disku:
to samé ale následující kód musí být uložen v ANSI (například v externím souboru x.php a do původního nahrávacího skriptu vložen přes include "x.php")

$search = array("ě","š","č","ř","ž","ý","á","í","é","ó","ú","ů","ď","ť","ň","Ě","Š","Č","Ř","Ž","Ý","Á","Í","É","Ó","Ú","Ů","Ď","Ť","Ň"); 
$replace = array("ě","š","č","ř","ž","ý","á","í","é","ó","ú","ů","ď","ť","ň","Ě","Š","Č","Ř","Ž","Ý","Á","Í","É","Ó","Ú","Ů","Ď","Ť","Ň");