Gentlemen, may I present: MultiCommander
. The link describes the 'Search' functionality from this freeware file manager, but there are a lot more things possible.
With Directory Opus it is pretty easy to find where the differences in a folder structure are. You can enable a function to automatically count the size of a folder and it appears very quickly in view next to the folder name. MultiCommander has similar functionality. While not as smooth as in Directory Opus, it does work. You can then use the dual pane view, point each of the pane to the folders you want to compare and start the folder size counter. Identifying which folder is different becomes pretty simple.
If you have often these kind of jobs, just as Directory Opus, MultiCommander has scripting
options and it allows you to create buttons that allow you to unleash (your own) scripts on the file(s)/folder(s) you have selected. Again, it isn't as smooth as Directory Opus in this regard either, but as freeware file managers go, this is a seriously impressive feature. You can even link batch scripts to buttons with the included editor.
Granted, initially it is more work to get the immediate job done, but I think that with a bit of digging and tweaking, you'll have a Swiss pocket-knife of a tool to do some serious work with files at the touch of a few buttons.