Yes, there's a list of 12 files the patcher says already exist.
\escapefromtarkov_data\sharedassets9.resource
\escapefromtarkov_data\streamingassets\windows\assets\content\audio\voice\missing.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\items\mods\barrels\barrel_mk16_254mm.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\weapons\akm\akmn_client_assets.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\weapons\akm\akms_client_assets.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\weapons\akm\vpo_209_client_assets.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\weapons\akm\vpo_client_assets.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\items\mods\barrels\barrel_mk16_355mm.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\items\mods\barrels\barrel_mk16_457mm.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\items\mods\charges\charge_mk16_fn_std.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\items\mods\sights front\sight_front_mk16_fn_std.bundle
\escapefromtarkov_data\streamingassets\windows\assets\content\items\mods\sights rear\sight_rear_mk16_fn_std.bundle
I deleted them from the copy of EFT(Live) I made and started the patcher again. It completes successfully (or without error at least), then I copied over the SPT AKI files as per the instructions. Once finished, launching everything results in an infinite loading screen.