If the document is well-formed (or at least well-formed-ish) you can use the DOM extension and xpath to find and replace all br elements by a \n text node.
$in = '<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
"http://www.w3.org/TR/html4/strict.dtd">
<html><head><title>...</title></head><body>abc<br />def<p>ghi<br />jkl</p></body></html>';
$doc = new DOMDOcument;
$doc->loadhtml($in);
$xpath = new DOMXPath($doc);
$toBeReplaced = array();
foreach($xpath->query('//br') as $node) {
$toBeReplaced[] = $node;
}
$linebreak = $doc->createTextNode("\n");
foreach($toBeReplaced as $node) {
$node->parentNode->replaceChild($linebreak->cloneNode(), $node);
}
echo $doc->savehtml();
prints
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html>
<head><title>...</title></head>
<body>abc
def<p>ghi
jkl</p>
</body>
</html>
edit: shorter version with only one iteration
$in = '<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
"http://www.w3.org/TR/html4/strict.dtd">
<html><head><title>...</title></head><body>abc<br />def<p>ghi<br />jkl</p></body></html>';
$doc = new DOMDOcument;
$doc->loadhtml($in);
$xpath = new DOMXPath($doc);
$linebreak = $doc->createTextNode("\n");
foreach($xpath->query('//br') as $node) {
$node->parentNode->removeChild($node);
}
echo $doc->savehtml();