Ok, amazing update :shock: :
I wasn't able to install the BC Patch 1.1 into the backup directory since I already installed it in the other install. I try changing the registry to see if I could bypass this, but it was to no avail. I then tried renaming the KM 1.0 BC directory "Bridge Commander 2" and putting the other BC directory (renamed "Bridge Commander") into the Activision directory, but the patch still refused to install. I tested the backup BC directory with BC 1.0, and it opened no problem. Then, just out of curiousity, I tried to again open the KM 1.0 BC install.
It opened with no error!
I tried opening it a few more times in case it was just a fluke. Still worked!
So apparently, if you use BC in Wine and come across a C++ debugging error after upgrading to KM 1.0, simply rename your BC directory to something else. Of course, I can't say 100% that that will actually work, since I also had restarted the laptop a bunch before trying this, and I also deleted this section of the registry when I was trying to make the patch work:
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Activision\Star Trek: Bridge Commander\V1.1]
"CD"="[CD path]"
"Comments"="Star Trek: Bridge Commander Patch"
"DisplayValue"="1.1"
"INSTALLEXEPATH"="[Path to STBC.exe]"
"INSTALLPATH"="[Path to BC folder]"
"Publisher"="Activision Publishing, Inc."