How to get dotCover coverage report from multiple test projects in Jenkins
Okay so I figured it out, apparently I didn't google quite enough beforehand. DotCover provides a guide to working with their commandline here: https://www.jetbrains.com/help/dotcover/Running_Coverage_Analysis_from_the_Command_LIne.html
What ended up working for me was using the method that they describe under "To run coverage for multiple projects in separate steps", running a batch command to get a coverage snapshot for each of the testprojects with each project having its own config file, then merging these snapshots and then reporting the result of the merge.