According to PWInsider.com, the reason why the old "WWF" logo was not scratched out on archival footage shown on Raw 1,000 is due to a new company directive updating the old policy of "censoring" out the WWF logo.
Sources within WWE are claiming that the use of the old "WWF" logo is now permitted in flashback footage, so short clips featuring the logo, which was banned from WWE use back in 2002 when the company lost a lawsuit against the World Wildlife Foundation, is now allowed.
Sources have noted that this new directive might not apply to longer archival footage and matches, but WWE is working on a strategy to eliminate the need to blur the old logo before the Network launches.