How Do I Let Guildwork Update Atma/abyssite?

I had this account on FFXIAH before using the guildwork plugin and mantually put all my abyssite and atmas. Well now guildwork will do it but I have no idea how to let it do that. I tried unchecking all of them and it changed the tooltip at the top of the page saying gw will update but it hasnt. I did /gw flush in game and still nothing. Any idea how to let guildwork update it like it does my merits automatically?

You shouldn't need to do anything for it. There can be two reasons for this:
1. It's currently broken. Always possible after an update. We know abilities shifted around, maybe key items did as well.
2. It saw you had all, and after you unchecked it it doesn't bother to check for them anymore.

There may be more reasons for it, this is what I could come up with just now. I've never used that feature myself (or not paid attention anyway), so I could also be misunderstanding how it works...