You were actually on exactly the right track with your first regex. The simple trick is to assign $1 to another var, modify that var, and then use the modified value as the substiution like this:
$html =~ s/\n/<br>\n/g; # assume this, and then fix <br> in pre block
+s with.....
$html =~ s{<pre>(.*?)</pre>}
{ local $_=$1; s/<br>//g; $_ }gse;
print $html;
We need the /g of course, the /s to make . match \n if present and the /e to exec the code in the replace block. The last thing evaluated in the replace block is what is used.
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