What I have done here in order to permanently disable the check box you want the code to leave alone is to use a custom data attribute "data-permdisable". This tells the code to skip making any changes to the element.
Also, I should point out that you should have checked="checked" and disabled="disabled" as a matter of form.
<input type="checkbox" value="1" name="malzeme1[]" checked="checked" disabled="disabled" id="checkboxExample1"
onclick="checkNumChecked(this, 2)" data-permdisable="true">
<label for="checkboxExample1">
So?an<b class="product-subtitlex"> | + 1 ?</b>
</label>
<input type="checkbox" value="3" name="malzeme1[]" id="checkboxExample3" onclick="checkNumChecked(this, 2)">
<label for="checkboxExample3">
So?anx<b class="product-subtitlex"> | + 1 ?</b>
</label>
<input type="checkbox" value="4" name="malzeme1[]" id="checkboxExample4" onclick="checkNumChecked(this, 2)">
<label for="checkboxExample4">
So?anc<b class="product-subtitlex"> | + 1 ?</b>
</label>
<input type="checkbox" value="5" name="malzeme1[]" id="checkboxExample5" onclick="checkNumChecked(this, 2)">
<label for="checkboxExample5">
So?anxc<b class="product-subtitlex"> | + 1 ?</b>
</label>
<script>
function checkNumChecked(ele, limit) {
var ct = 0,
siblings = document.getElementsByName(ele.name),
checked = 0;
for (ct = 0; ct <= siblings.length - 1; ct++) {
checked += ((siblings[ct].getAttribute("data-permdisable") == "true") ? 0 : ((siblings[ct].checked) ? 1 : 0))
}
for (ct = 0; ct <= siblings.length - 1; ct++) {
siblings[ct].disabled = (siblings[ct].getAttribute("data-permdisable") == "true") ?
siblings[ct].disabled : siblings[ct].checked ? false : (checked == limit) ? true : false
}
}
</script>
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