In QGIS, I had a larger DEM that captured the lake surface and a smaller DEM of the lake bathymetry. I spent a while trying to figure out smart ways to combine the two so as to replace the DEM lake surface with the bathymetry. What worked is using the GDAL merge because it apparently favors the last of the overlapping rasters and the bathymetry happened to be last. If that helps anyone else in my predicament then this post will be worth something.
However I am curious if there is a "better way" to replace the values in one raster file with overlapping values in another (the order of the raster in merge seemed slightly arbitrary and hard to control). It seems so incredibly basic a task I am sure there must be some simple function I am overlooking.
This is very similar to this post, however, the answer would not work as it outputs a raster the size of the smaller bathymetry DEM.
The Saga Mosaic Raster tool with "minimum" set for the "overlapping Areas" also seemed promising, but so far it seems that the tool is broken. I either get incorrectly shaped files or a raster without CRS info. I can't make head or tail of it.