$ cat foo.txt 
one
two
three
$ perl -wMstrict -pe 's/^t(?!h)/th/; s/(.)\1/$1/g' foo.txt > bar.txt
$ cat bar.txt
one
thwo
thre
$ perl -wMstrict -pe 's/th/ph/g' -i.bak bar.txt
$ cat bar.txt
one
phwo
phre
$ cat bar.txt.bak 
one
thwo
thre