After running the updates, all of the fixes are still there
Of course they are still there, that's the whole point of the updater recognizing the fixes: the OrbX fixes are files not made by FSDT that older versions of the Live Updater would have removed.
except for the two files I mentioned. They are nowhere to be found. Are they even a part of version 2.1?
It seems you still don't understand.
Part of the process of installing the OrbX compatibility fix, other than adding the files made by OrbX, is to DISABLE those 2 files that belong to FSDT KLAS, with the process you said you knew how to do: renaming them to .OFF
The FSDT Live Update found you had the OrbX files installed, and DISABLED THEM FOR YOU, by removing them. That's why you don't find them, the Live Update has already done what you are supposed to do manually!