I believe that part of the problem stems from the fact that the game came on two CDs (which are now two directories in the game's installation directory). These two CDs include files with the same name, but containing different resources.

[Edit: I just looked at the installation that GOG Galaxy installs, and it would appear that the two CD directories no longer exist. I do not know if that means that the game is now permanently broken, because the duplicate file names with different data were ignored when making this copy, and thus only one set of the files has been preserved. If so, this would be a major issue, and negates my discussion of how DosBox might work (below).]

I know that the game runs in DosBox, and that DosBox is capable of mounting both directories as drive D: and E:, however, there are two things I do not know:

I do not know if the game can recognize that both CDs are mounted at the same time, and switch between them as needed (some games were programmed by people who assumed that you had one CD drive, drive D:, and could only "see" a CD if it was in that drive). Apparently there is no notification (none of the posts I've read, nor my own experience with the game, have shown that anyone was notified that a disc change was required); and, I do not know if it's possible to tell DosBox to unmount one directory and mount the other one, at appropriate times, as the game was originally set up to do.

As it is, it would appear that the game looks for files on D: first, and only looks on E: (assuming this is how it's set up) if it does not find files by that name on D:. Since it does not ask you to swap discs, I'm assuming both are mounted, and the game knows that both are there.

This is a technical issue that, it would seem, would require some work on the part of both GOG and the DosBox developers. Whether there is any incentive for either of them to work on a solution, I do not know.

I read somewhere that there is a patch to bring Betrayal in Antara up to Version 1.1.0 (just looked, and the current GOG version is 1.1.0). Supposedly it addresses several issues, including this one, but I will have to do some more research.

I hope this clears up some of the confusion as to what the exact problem is. I wish GOG would let us know that they are interested in finding a solution for us. I would like to complete this game, myself.