If I understand this correctly (and I hope I do) you used to get a region rendered in batch which was automatically placed in the correct coordinates in compositing?
If that’s the case, after the changes that affect this, there’s an option in Render settings > Common tab > Image FIle Output > Image format Option > Data window. If you set this to “Whole image”, the data window coordinates will be of the full image.
If it’s easier to not open your scenes, tweak the settings and re-save them, you can add a preRender script to deadline to set the option for you:
-preRender "setAttr vraySettings.imgOpt_exr_autoDataWindow 2;"
For example
<path_to_maya_batch> -r vray -reg 0 500 0 500 -preRender "setAttr vraySettings.imgOpt_exr_autoDataWindow 2;" <path_to_scene>