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Ok, i have searched, and couldn't find anything, so please don't shoot me if i missed something.

My confusion is: in the new version of 40K, Command re-rolls are limited in what you can use them on, page 255 of the main rule book.
One of the things is re-rolling the dice to determine the number of attacks made by a weapon.

Most of the deamon weapons available to Chaos Lords and Deamon Princes have a mechanic where you roll a D6 and if its a 1 you can't attack with that weapon, and if its a 2+ you add that number of attacks, so this would seem to be a die rolled to determine the number of attacks made by the weapon, either zero or 2 to 6.

So since this is not explicitally part of the weapons profile (like shots on a flamer), is this covered by Command Re-roll or not?

In the beginning paragraph of the Daemon Weapons section. It specifically mentions rolling the dice to see if it works. Any affects beyond that is the weapons specific effect. Therefore you cannot use the command reroll on the daemon weapon.

^
If the daemons weapons profile was "Melee D6", then yes you could command reroll. However its doesnt have that and as mentioned previously, the extra attavks are just an ability of the weapon.