Your original post implied that the files were empty when you call prerequest2.pl, but if they have some content then the error situation is actually completely different. Please see "How do I post a question effectively?" and follow the suggestions there (such as providing sample input and expected output) so your posts are more helpful to those providing help.

How many lines are there in your input? Have you tested your conditions and other parts of the code (xpathconfiguration.pl, domain_check(), and the grep) to be working? I'd suggest printing some debug output in your innermost loops to see what actually gets written to the file. Also, see Basic debugging checklist