I sent a support ticket but was pointed towards the forums instead:

I have been playing FFXIV on Gilgamesh since beta - A few days before the latest patch I completed gathering enough light for the Nexus, after what is pretty much two months of work feeling ready to the new relic quest.
Upon going to the NPC to turn my gear into its Nexus form, only the Sword is eligible, even though I've had both the Sword and Shield equipped at all times since they were turned into Novus.
I learn that the Shield also needed to be soulglazed in order for it to gather light at the same time. At the time of the original soulglaze, it wasn't made obvious that one needed to apply it to both items since the items themselves do not change (unlike Atma to Novus form, which is nearly impossible to miss) and upon inspection of the zodiac glass and the light gaining text, it looked like gaining light was working fine (did not expect to have 2 texts show up for Sword and Shield separately, since all classes have only 1 show up, I didn't even think about it twice), so I though nothing of it until now, since it looks like it forces me to redo EVERYTHING from the start with the shield.
I don't want all the work and time I put into it go to waste or have to spend the same amount of time and effort to get the shield up to par. This issue only exists on Paladin, all other classes have a single item to soulglaze and gather light for, so this is really the only class where something like this can even happen.
Now that the patch hit, I'm barred from continuing the relic quest because of not having clicked on something months ago, since it won't let me start the quest with my weapon only. I find this to be much too punishing since it would require countless more hours put into something that I've already accomplished and once again such a thing would ONLY ever happen on the Paladin.
Something should be done so that this doesn't happen, like have both items soulglaze at the same time and turn them in at the same time, like so many other upgrades in the game (the tome ones are the obvious examples). There is literally no reason to separate them since it's not like you can continue the quest with a single item - or else i would totally just have moved forward with the sword only. The soulglaze part is just badly build.

Most of the other things asked for in the bug thread are irrelevant, so I'll just post the relevant ones:

World name: Gilgamesh
Character name: Alessandra Floriani
NPC name: Jalzahan
Class/Level: lvl 50 Paladin
Party or solo: Solo
Area and coordinates: North Shroud