Put in markers on the first pass, then replace the markers on a second pass:

$newline =~ s/(\b$currword(?:ed|ing|al)?\b)/\$hashme\{$1\}/ig for @wor
+dlist;
$newline =~ s/\$hashme\{(.+?)\}/\\footnote\{$1 $hash{lc($1)}{explanati
+on}\}/g
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