JOSM: Splitting massive ways efficiently

Currently I’m working on importing the Canvec tiles that make up Lac Seul in NW Ontario, Canada into OSM. Importing the data as it is, split into tiles and subtiles, is poor practice, and manually merging is time consuming and dull. So I began using JOSM’s Join Overlapping Areas feature. This tool however requires that all ways be complete before merging. Resulting is a 100 000 node area that far exceeds JOSMs import limit and is time consuming to split up, and slows down JOSM. Is there an faster way to split this? Or to do manage tiled lakes in a more efficient way (as opposed to merging manually?)