Oh hey, It's you again Jimm~!
You make all the best plugins, you are just the best!
On to my question. Is there a way to configure the plugin to have it rename the stylesheets and other merged files? I think it's a quirk of my android epub reader app (Moon+ Reader Pro) that it doesn't handle same-name files in different folders very well. It works fine if I manually edit them in calibre's editor to rename all the covers, stylesheets, and pagestyles so they aren't the same (sequential numbering or whatever). Otherwise it just keeps reusing the first instance.
Just double-checking since I don't see an option that jumps out at me as being for this and it's not the largest of hardships to manually batch rename my occasional epubmerge.