Affiliate Marketing Secrets

I recently went to MEPS and after 3 continuous days I was able to get my NAVY CTN rate that I so badly wanted. I have a clean background; I’ve been cleared for a California Guard Card twice and worked for the LA Sheriffs Department for 2 years which required an extensive background check. My problem is that I was recently Laid- Off from my job as an Intern at a Financial firm. 2 other employees were also let go but they were more disgruntled and decided to delete contact lists, company files, marketing material on their computers before leaving. I left on good terms, but just a few days ago I received a notice from my previous employer that “I had attempted/proceeded to delete company files on my computer, though everything was recovered.” It’s completely unfounded as I left my computer untouched after I was given the notice to leave the premises. The letter I received was from the In-House legal attorney claiming that I had ‘attempted’ to do this though theres no real evidence to support their claims and they admitted that everything was recovered.
My question is how should proceed after receiving this notice and will this affect my background investigation for Top Secret clearance because I consider it to be ‘defamation of character’ and ‘libel’?
I have a clean background, no drug usage, good credit and feel that this minor accusation may lead to problems during my background investigation. Can anyone out there help me?