Yes I did not doubt that you sent an e-mail to FIFA. For me, the strange part was FIFA, not the Libya FA. FIFA did not put the match on their website until after the match was played. However, if they had your e-mail 4 days before the match, then the match should have been on FIFA.com.
The attachment from Mali clearly says "équipe nationale locale" - but for some reason, the Malians did not know the venue of the match they were playing in. :-/
Did Libya want the match v Jordan to count as an A match? That would be different if Libya agreed that the CHAN team should count as the A team. As you know, Libya FA can simply write to FIFA and the match will be removed.
I tried to tell FIFA that including CHAN matches was a bad idea. But they had a meeting, and made a decision and they don't like people telling them they are wrong.
You are right - teams like Ivory Coast and Nigeria (with not many home-based players) will suffer in the ranking. Teams with mostly home-based national teams (Sudan, Tanzania, etc.) will benefit.
In my opinion, CHAN matches are restrictive (in the same way youth matches or Olympic matches are restrictive). The only difference is that the restricting factor is not age, but the league in which they play. For teams ike Djibouti and Comoros, the CHAN national team will be almost 100% the same as the normal national team, but for Ivory Coast and Nigeria, for example, the CHAN team would be more like the C team or D team.