Yes it will.
But the good news is that you are warned twice before updating, giving you plenty of opportunity to remove the mods before the update.
The launcher asks you before downloading the patch, and then the patch installer asks you before updating the game files.
So it's a non-issue.
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11 War Patrols / 56 ships sunk or damaged for 212,022 tons
Zero casualties throughout the war
Scuttled on 8 May, 1945 in Sonderburg Bay, after German surrender
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