First of all I love me some Batch Update Threads. It's saving me tons of time right now. However, I notice when you choose a origin node it shows you every prefix available and not just the ones available to the node or nodes selected. The same thing happens when you choose the destination node. This can lead to a lot of scrolling in a tiny box on sites that use prefixes a lot. With inline editing on the front side it limits it to prefixes available to the node selected. So my suggestion is to limit prefixes to those available to the node chosen.
Also it will not updated the files if you choose a prefix not available so there is no reason to display them. Plus not displaying them can let you know you need to fix that issue as well.
To accomplish that, they'd have to change it to where you select a destination forum before selecting the prefixes to add. Creates an extra step. Alternatively, it could be done with ajax, when you change the destination forum it would have to repopulate the list. Definetely do-able and I can see how it'd be nice.