Novus and Nexus uses the same Sphere Scroll?

[Ladon]

They are not the same, and yes you will not be able to use a Novus scroll on a Nexus so make sure to apply the scroll you have before you upgrade (assuming you have made changes to the stats). If you haven't then don't worry, you can just discard the Novus scroll and generate a new one from the Nexus. Basically a Novus scroll has 75 materia slots where a Nexus scroll will have 78 slots (this is auto-scaled though, you don't need three extra materia for the Nexus). This is the reason there are two different options for scrolls.

Keep in mind that there is no real reason to have a pending scroll anyway as it costs nothing to apply and generate scrolls.

Edit: Oh yeah as pointed out it does cost tomes to generate a scroll. Had forgotten this as the cost seems so insignificant in the grand scheme. The first paragraph still applies though.