I have created a bunch of map tiles for Google Maps mistakenly using the Google Earth projection. Is there a tool available to batch warp the KML files to the correct projection or will I need to generate the tiles again from scratch?
Check out the open-source GDAL/OGR utilities - (the OGR part) http://www.gdal.org/ogr2ogr.html
ogr2ogr.exe is a command-line tool which can be used in the FOR loop in a batch file to go through all your files and transform them. (for example in windows you create a *.bat file and put your DOS code for looping there).
In the OGR link above there is also a nice example for reprojecting a shapefile, you can apply it to your KML file.