Well it needs to check your whole game for references to the rpk you are trying to merge that means it loads all rpks and scans all the scripts (which can contain errors but it will only touch the ones needing touching...) it also reports errors it finds that can affect its ability to find all references (it probably is cluttered with inconsistency errors for scripts those don't really matter because if the java is present the program will update that and the game can compile it) the typeID collision errors mean that there are entries in an RPK whit the same typeID naturally if something references such a TypeID it does not really know which is referenced.
Nevertheless nothing happens until you press the last (rightmost) button and when you press the second from the right it will report at the and of the operation exactly which files will be modified (After the line:
The following files and folders will be updated if the current operation is run:
)
there you can see whether it is reasonable or not (it most likely will be correct thou as I said I used this extensively during the development of SlrrExhaustive)