It should work. The following code works fine:

#!/usr/bin/perl -w
use strict;

   while (<DATA>) {
       if (/aaaa$/) {
           local $/ = '%'; # use local here for extra-cleanness ($/ is
+ restored to its previous state when you exit the block)
            while (<DATA>) { print "read: $_\n"; }
       }
   }
__DATA__
XXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXX
XXXXXXXXXXXXaaaa
abcdefghijklm%nopqrstuvw%xyz
[download]

The problem must be somewhere else in your code.

This is actually one of my favorite tricks, it always impresses people who don't know it ;--)