Just as a heads up to anyone else who finds this and had the same issue, the FM needed a patch to run on NewDark, (the upgraded engine).
Here is a link to the thread which has a link to the Google Drive repository of FM fixes.
If you follow that link and download the Calendra's Cistern fix, and then unzip it into your Calendra's Cistern folder, (in your mod manager), and then restart the mission, the issue should be fixed. It worked for me anyway.