You have to be very careful with the "Move children to output" option. That will automatically create new names under the output genus.

e.g. Neomarica caerulea would automatically become Trimezia caerulea. In many cases that automatically swapping will create invalid new names. In this case, in POWO, it is spelled Trimezia coerulea, with an o: http://plantsoftheworldonline.org/taxon/urn:lsid:ipni.org:names:441647-1

So you first need to check if all the epithets line up exactly, do the species taxon changes for the cases where they don't line up, and then you can swap the genus.