This all boils down to an interpolation problem. In your second run, your '\?' substrings are interpolated into mere '?'.

Try perl -e print "WTF\?\?\n". You should wind up with a return of WTF??.

So WTF?? does this have to do with the problem above? Well, $matchtext = "http://www.new.site/somenewpage.pl\?\?" interpolates to http://www.new.site/somenewpage.pl??. So you are running this regex: s#http://www.new.site/somenewpage.pl??#http://www.new.site/somenewpage.pl?:. Which isn't intended at all.

Use a non-interpolating quoting mechanism like q// or '' when you specify your $matchstring and your $replacestring. Also note that things like ?.* are safe in the second half of a substitution, of course you'll still need to escape \ and whatever character you are using as a delimiter (typically /)

TGI says moo