That sort of belies your claim that $file2 doesn't exist. From the information you gave, there is no way to tell which directory the soft link was created in and which directory you did the ls in. If the file name of the soft link is "/a/b/my_link", and you ran your program in the directory /programming/perl/ and you did the ls in the same directory as the one in which you ran your program, then ls won't list the link. But when you do the test -e "/a/b/my_link", it will return true.

You might want to read the details of man ln to see if you can spot what happened. Or you might simply want to try an ls -al.