Just did find ~ replace \n on a 600kb file, about 4000 replacements.
Works fine on WinXP,SP1 with TextPad version 4.7.2.
Perhaps try the latest version?
HTH
Then I open up and see
the person fumbling here is me
a different way to be
I just filled a file with 80000 (eighty thousand) lines of 100 ~
making altogether 8000000 (eight million) ~ characters,
then I replaced the ~ with \n.
It took some time (about 15 minutes), but then I had a file with eight million eighty thousand empty lines.