In the time between submitting the first draft of a paper to a journal and submitting the third and final version (now), my institutional affiliation has changed. Should I indicate my original affiliation on my (latest) submission, or my current affiliation? All the work for the paper was done while I was at the previous institution.
Ask the editor which they prefer, but (IME) the most common approach is to give your old institution (the one at the time of submission) and add a footnote saying "Now at...". An alternative would be to give two affiliations. Omitting your old affiliation entirely would seem strange.
(Bear in mind this may well vary substantially between disciplines, as with almost everything else! Again, if in doubt, ask the editor. It's their journal, after all...)