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On Plesk for Linux mod_status is disabled on upgrades to improve Apache security. This is a one-time operation that occurs during an upgrade. You can manually enable mod_status later if needed.
I think this is normal Plesk behaviour. At least the same thing happens with OBAS. I assume he can select both subscriptions, right? If so, it's perfectly normal behaviour and the second user/pass combination is for FTP access to the specified domain.
Can you try testing the following: https://domain.tld:8443 with username: the main website/FTP access username and password: that username's password? It should work, though I'm not really sure as I don't have WHMCS installed.