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Every time i create a new set it reassigns my Keymaps. it always gives me the following

FFXIV-# Always on, FFXIV-# Combat, FFXIV-# Non-Combat.

the # increases with each new set, FFXIV-2, FFXIV-3, etc... and then i have to remake new keybinds since they don't exsist in that set. Is there something i'm doing wrong, or way to force it to use another set that already has the extra keybinds i made? It warns me if I use any current Keymaps that it may break my other sets

It usually gives you that warning when you set hotkeys (or don't set hotkeys) in the wizard that are different to those configured in the already existing mapped keys (the default ones that the wizard creates).
You can always just use the current key maps and then it wont create new ones. Just be aware that some mapped keys may be overwritten if you select this option.