How to expand SharePoint locations with 5000+ items
If you have SharePoint locations having more than 5000 items directly in that location when you try to expand location in ReplaceMagic you will see following error message:

To create correct index go to your SharePoint location where you have 5000+ items. For example:

and click on
which will open:

where you need to click on "Library Settings" and, as you can see in screenshot, we have document library with 732558 documents (and threshold limit is 5000):

Scroll down on that page where you will need to click on "Indexed columns":

where you will have option to create new index:

To enable drill-downs you will need to create index on column "Content Type":

As index creation will take some time when it is done you will see:

and ReplaceMagic will be able to drill down those large locations.
More infos over Microsoft site: https://support.office.com/en-us/article/manage-large-lists-and-libraries-in-sharepoint-b8588dae-9387-48c2-9248-c24122f07c59