Opacity information is held within the at5.xml file, and I believe that only one of these will be read (and also, possible, that it has to be in the root folder? Can someone confirm?).
The simplest solution, if you maps are contiguous (sounds like they are), is probably to export both maps together. This will take a while, of course, but once you have your shaded relief folder you might be able to skip the raster export in future and just export the vector layers, which will be much quicker (again, export both maps together).
Edit to add: to export both maps together, multi-select them in the asset list and use the right-click export function. This capability is new in RM2.