I am currently cleared with a 3 letter IC at the TS/SCI level with ci poly but need to upgrade to the FSP level for more access with them. Does this mean my entire clearance goes through adjudication again meaning that my current ts/sci ci poly that i have with them will have to get adjudicated again? or just the FS poly part that i dont currently have?
Probably… and this is just a ‘probably’ you will just need to wait for the FSP to be favorably adjudicated or whatever the correct term is.
Probably 
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FWIW, when I did my poly, it was well after I got my full TS. All they did was schedule me for it then add it to my epas when it was done. They didn’t need to do anything with my clearance. I think they are separate processes.
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Just need to do poly.