What do you mean by "decided to update before I rendered it, " you have updated Natron ?
I think you need first to find what node is acting weird, is that bug show up in the viewer ?
If not, it may come from a wrong alpha channel, try to put a shuffle node right before the write node, with settings RGB (no changes) A -> 1
if the issue is visible in the viewer, then look at all the nodes and see where this bug is happening ...
may the force be with you !