if you want to move a file around from within maya you can use the sysFile command. http://help.autodesk.com/cloudhelp/2015/CHS/Maya-Tech-Docs/Commands/sysFile.html so you would use the -rename flag with sysFile - eg: sysFile -rename "C:/batchTest/pew.obj" "C:/batchTest/POW.obj"; //This renames pew.obj to POW.obj
It should rename the target UV map when you rename the UV map. But be sure that the high and low UV map names are different, otherwise it'll try and bake both. Bit annoying.