No guarentees that it will catch every situation, especially as the acknowledged experts are tripping up, but this is my attempt. It seems to work for most cases I can think of and seems somewhat simpler than some of the others.

$_= '1 <% xxx%%> 2 <%%> 3 <%>%> 4 <% >% %> 5 <%%%% xxx %%%%> 6 '; 

s[ <% .*? (?> %> ) ][!REPLACED!]xg; 

print;

1 !REPLACED! 2 !REPLACED! 3 !REPLACED! 4 !REPLACED! 5 !REPLACED! 6
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