I have no idea what you're getting at, because this code looks like Perl, and maybe smells like Perl, but it sure as heck won't run. It appears to be missing major parts. For example, where is $file assigned? How do you read two files with only one file handle?

use strict and -w. Begin with something like this:

#!/usr/bin/perl -w

use strict;

# (More program ...)
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That being said, you're probably going to get a whole ton of warnings. For instance, you're trying to use a string as an array reference. There's a comment with no comment prefix.

Don't get ahead of yourself. Read in the changes file first, and then worry about the rest. Now here's an idea on how you can read it in.

open(CHANGED, "changed.txt") || die "Can't open change log\n";
my @changes = map { chomp; [ split('-', $_) ] } <CHANGED>;
close(CHANGED);
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This makes an array of arrays (AoA). You can read this like you expect with the rest of your code. If you want to put this in a hash, like you've suggested, thus making a hash of array of arrays (HoAoA), try using this in the loop:

$changes{$file} = \@changes;

Now that you've got the data, the rest should be a lot easier.