$uniq{"$file"} = ({"suffix1"=>"$suff"}); 
$uniq{"$file"} = ({"suffix2"=>"$suff"});
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You overwrite the first hashref (for suffix1) when you assign the hashref for suffix2.

# assign hashref with first key-value-pair
$uniq{"$file"} = {"suffix1" => "$suff"};
# add additional key-value-pair
$uniq{"$file"}->{"suffix2"} = "$suff";
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perldoc perldsc should show you how to create complex data structures.

edit1: syntax error fixed

edit2: "perldoc perldsc" as link text

edit3: "edit" history edited