Indeed, and after some tests I found you can make this game run without having to mount the CD subdirectory as the CD drive, and no matter what path it is located under. Here's how:
Move everything from the \CD\ subdirectory - including the CONQUER subdirectory - to the main game directory, but
do not overwrite the existing conquer.ini. Overwriting a duplicated GOB file is OK. You can now remove both batch files (optional, but they're useless from now on). Now, change the paths in conquer.ini to:
Code:
GOB=.\
AUD_DRV=.\
CD_PATH=.\CONQUER\
Ta-dah!