..the following is not wise nor beuatiful, but it works (added some space for readability and please note windows double quotes!)

cat lorem.txt

Lorem ipsum dolor sit amet, consectetur adipisci elit,
sed do eiusmod tempor incidunt ut labore et dolore magna aliqua.
Lorem ipsum dolor sit amet, consectetur adipisci elit,
sed do eiusmod tempor incidunt ut labore et dolore magna aliqua.


perl -M"5;$S=shift;$R=shift;open $o,'>','new2.txt'" -ne "chomp;if($_=~
+/$S/){print qq/$_ $R?/;($_=$_)=~s/$S/$R/ if<STDIN>=~/y/}print$o $_.$/
+"  ipsum REPLACE lorem.txt

Lorem ipsum dolor sit amet, consectetur adipisci elit,  REPLACE?   y
Lorem ipsum dolor sit amet, consectetur adipisci elit,  REPLACE?   n

cat new2.txt

Lorem REPLACE dolor sit amet, consectetur adipisci elit,
sed do eiusmod tempor incidunt ut labore et dolore magna aliqua.
Lorem ipsum dolor sit amet, consectetur adipisci elit,
sed do eiusmod tempor incidunt ut labore et dolore magna aliqua.
[download]

L*

PS after some failure I gave up passing regexes as arguments and toying with perl -s ... -S=ipsum and whatalike

PPS add -MO=Deparse to see it better:

perl -MO=Deparse -M"5;$S=shift;$R=shift;open $o,'>','new2.txt'" -ne "c
+homp;if($_=~/$S/){print qq/$_ $R?/;($_=$_)=~s/$S/$R/ if<STDIN>=~/y/}p
+rint$o $_.$/"
sub BEGIN {
    require 5;
    ()
}
$S = shift @ARGV;
$R = shift @ARGV;
open $o, '>', 'new2.txt';
LINE: while (defined($_ = readline ARGV)) {
    chomp $_;
    if ($_ =~ /$S/) {
        print "$_ $R?";
        ($_ = $_) =~ s/$S/$R/ if readline(STDIN) =~ /y/;
    }
    print $o $_ . $/;
}
-e syntax OK
[download]

PPPS given perlrun doc inaccurate on -s switch

perl -M"5;open $o,'>','new2.txt'" -sne "chomp;if($_=~/$S/){print qq/$_ $R?/;($_=$_)=~s/$S/$R/ if<STDIN>=~/y/}print$o $_.$/"  -- -S=ipsum -R=REPLACE lorem.txt

..works!