I need to replace this list with a list of "features" of those names, that come as the output of a function

Then you need map, not grep. However, s/// doesn't play well with either unless precautions are taken, so it's simpler to use for here.

my @newlist = @oldlist;
s{(\d+-PVC_\d+)}{ function1($1) . '/' . function2($1) }e for @newlist;
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You were clobbering @oldlist.