It's been a few years now that I've been using the method of take-home compositions and more particularly by disabling "single folder (flat)" to keep the structure of my subfolders. I change the root path by doing "select/replace" > choose the "save to folder" column and replace one value with another (for example: replace "c:\...\...\...\folder" with "c:\folder")
However, I've had a problem for some time, I'd say since the 2015 SP3 version (still relevant with the SP4): When I use "select/replace" to remove unnecessary subfolders, SW crashes systematically!! I tried with different assemblies, going through SW explorer (and disabling the Workgroup PDM add-in)... Nothing helps! It's annoying.