Update: The 500 legion resources re-appeared about 2 hours after finishing the last one, didn't need to do all other 3 missions (1x of each) for it to re-spawn.
I just finished my 500 Legion Supplies mission and I know / was told they re-appear once you either
1) Do them
or
2) Do all of them.
That doesn't seem to be the case of now, I relogged and everything and it's been 15 minutes.
Right now, I finished the resources, 10 hours left on the nethershards and the AP one is still there, untouched.
Should I wait more?