I'm not sure why you added the update. I don't see what it adds, and it's not true. /\bChi_2\b/ will match plenty of strings.

'Chi_2'   =~ /\bChi_2\b/  # Match
'!Chi_2!' =~ /\bChi_2\b/  # Match
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Maybe you had a specific string in mind, but I don't see how this relates to the OP. He would not use Chi_2 in the regex pattern.

In a world where an identifier matches /^\w+\z/, you might do something like

($_ = '\\Chi+3'  ) =~ s/\\Ch\b/$ch/g;      # Won't replace
($_ = '\\Chi+3'  ) =~ s/\\Chi\b/$chi/g;    # Will replace
($_ = '\\Chi_2+3') =~ s/\\Chi\b/$chi/g;    # Won't replace
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But what if identifiers match /^[a-zA-Z]\z/? You'd want the following behaviour:

($_ = '\\Chi+3'  ) =~ s/\\Ch???/$ch/g;    # Won't replace
($_ = '\\Chi+3'  ) =~ s/\\Chi???/$chi/g;  # Will replace
($_ = '\\Chi_2+3') =~ s/\\Chi???/$chi/g;  # Will replace
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That's the OP's question.

As I've already mentioned, I recommend extracting the identifier, then checking if it's one of interest. This can be as simple as the following:

/\\([a-zA-Z]+)/ exists($vars{$1}) ? $vars{$1} : "\\$1" /eg
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The technique scales well, and it avoids the problem of matching something you've previously replaced.