Firstly the patcher isn't auto. It asks you if you want to install the patch.
Secondly, how is this any different from past SH games? Whether the patch is applied manually or downloaded by UBI it still has the potential to overwrite mods.
I think whether you are using SH3, SH4 or SH5 if a patch is released for any of these games it would be prudent to ALWAYS patch the STOCK files. i.e when a patch comes out - remove all mods first.
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