You thought the second match would use $line because the first did. It didn't. You didn't provide a target for /PatternEnd/ so it bound to $_. Write it using the second example I've quoted.

# You wrote
if ( $line =~ /PatternBegin/ .. $_ =~ /PatternEnd/ ) {

# You wanted.
if ( $line =~ /PatternBegin/ .. $line =~ /PatternEnd/ ) {
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