Yes, if you change chapters within a campaign or change campaigns entirely your change mods. Make sure to change mods before you change chapters.
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Update on objectives:
I got a finished on "Patrol area assigned. Reach the area AM5197 and start operations. Attack any enemy contact" and then got a coded message to a new patrol area and finished "New orders 1". Then I got a "New orders 2" but that's ongoing despite not receiving any coded messages.
I'm guessing New orders 2 is my third and final patrol area and I never received the coded message telling me where it is.
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