With the 0.6.0 version I hope I fixed scenario two.
scenario #2 is now fixed!
for scenario #1 I think the way your program works now is that it merges spanned files IN THE SOURCE. This is not good since usually the source will be full and thus give you fail result, also it it slow.
I think you should program it to do the merging process in the destination folder.
Also its not so clear, but is there an option that the sources will be left or just copied and not moved? For safety reason.
I think you have that but I guess the option words are not clear to me , sorry.