What counts as an outcome of a grant? When one goes from one grant to another, there are a few papers that are in the pipeline during the process. I have one such paper that was in submission when I switched grants. Submitted on the first grant, and then revised and resubmitted on the second and with additional changes on the second. This paper was then accepted. I acknowledged both grants in the final transcript as work was done to the paper on both grants.

The second grant agency asks for updates of research outcomes and consequences during the grant in a very black and white way of listing publications that are a product of the research. Is this paper considered a research outcome to the second grant?

This is in mathematics, if that helps, and there was some math to be done to fix the referee's complaint(s).
The rule of thumb that I generally use is that if any portion of a work has been supported by a particular grant, then it counts as part of the outcomes of that grant.  

Typically, in reporting on outcomes, one is asked not just for names of papers, but also for some sort of narrative of the work, in which it is simple to state what work was done, much as you just did.  If for some odd reason the funding agency only wants you to list papers and nothing else, then I would think that it is incumbent upon them to understand that they may not be the sole source of support for some of the items listed.