@AsherIf you select only one map at a time then only that map is converted. When this is however a map pack, the entire pack is converted map by map but into the same folder, same as its source.
Sorry, could not help it - just made another release 1.8.0 that provides better entity conversion support including automatic suggestion of most likely replacement and a few other improvements (e.g. @vladislavbelov's tree randomization script).
One new architectural thing is that I extracted a common code package that will be also used by other ATLAS-related tools that I am preparing.
Please find the latest release 1.8.0 in the top message of this thread (with updated screenshots)