Hi, you can not apply sen2co to a subset of a S2 data product. This because sen2cor can only work with S2 data organized in the .SAFE format , while a S2 subset can be saved for example in a .DIM format but it is not possible yet to save a subset with the original S2 format. What you can do is only to process the full S2 product with sen2cor and only after that you can define your subset with atmospheric correction.
I hope I didn’t sat anything wrong @marpet @obarrilero