Hi! First of all, the code is a bit chaotic/messy IMO. I suggest that you work with a bit more whitespace and subroutines. Thats of course a matter of style, but a cleaner style often leads to easier discoverable bugs.

To the code: I've read through it mostly and one line was IMO fishy (see around line 109):

         for (@array) {
            s/$inputline3/$encryptpw3/g;
            print ("\n\nYour Username and Password have been updated a
+nd saved!\n\n");
         }
[download]

$inputline3 contains the entered password and not the encrypted password. Is that maybe a mistake? Also note that if the username is the same as an encrypted password, it will also be replaced with the new password. I suggest to make the substitution more precise:

   s/^([^:]):\Q$encryptpw2\E/$1:$encryptpw2/
[download]

The \Q...\E is just for the case that $encryptpw2 contains '.' or '\s+' or '[' or whatever character might have some other meaning in a regex.