Affiliate Window had a big glitch a couple of days ago where lots of confirmed and rejected transactions went back to pending.
They asked merchants to process them all again.
In theory if it was previously approved then the merchant should obviously approve it again.
Perhaps the merchant you are referring to thought they were duplicates and rejected them not realising what had happened with the glitch.
Don't panic yet!!
Just chase
AW and tell them that previously approved sales now show as rejected. Could be an honest mistake.