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What do you mean? From what I know, "proton files" refers to, basically, "emulated" virtual Windows filesystems which the game ran through proton uses, so it stores things like the savefiles, logs, the directx/.net dependencies installed if there are any, and so on. Being that the case, deleting the proton files would also delete the saves unless the game has Steam Cloud and it's online at some point so they can be synced beforehand (and OP was offline).
Every game without Steam Cloud that I remember deleting the proton files started from scratch after doing so.