If you want to only swap in values that exist then use the following:

s{(<\?--(\w+)-->)}{
    defined($swap{$2}) ? $swap{$2} : $1
}eg;
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That will only replace values that match have a corresponding entry in %swap.

If you are brave you can use something like this:

s/<\?--(\w+)-->(??{ defined($swap{$^N}) ? '(?=)' : '(?!)' })/$swap{$1}
+/g;
[download]

It also does what you are looking for - but without the e modifier on the swap. You will probably need to read perlre to follow it fully - but essentially you are using the (??{}) block to check your regex as you go and then using ?= and ?! to report success or failure.