$string =~ s/[^<B>]($swapString)[^<\/B>]/<B>$1<\/B>/gi;

##</code><code>##

[^<B>]  <- this matches any *single* char that is not a < B  >
($swapString) <- this put the match for $swapstring into $1
[^<\/B>]  <- this matches any *single* char that is not a < / B  >

##</code><code>##

$string =~ s/([^<B>]($swapString)[^<\/B>])/<B>$1<\/B>/gi;

there is a <B>foo bar</B> and a <B>bar foo</B> and also<B> foo </B>and<B> bar.</B>

##</code><code>##

$string =~ s/(?<!<B>)($swapString)(?!<\/B>)/<B>$1<\/B>/gi;

# this gives:

there is a <B>foo bar</B> and a <B>bar foo</B> and also <B>foo</B> and <B>bar</B>.