You can use the CodeWarrior Command Window tool (CodeWarrior menu->View->Command Window) for flash programming operations from the command window. You can also create a command window script for automation purposes.
Please use the Command Window help documentation as a separate document for this is not available. For the beginning you can type "help fl::" in your Command window and after that press the "TAB" key. You can see all commands available for "fl", for example "help fl::blankcheck", "help fl::checksum", "help fl::write" and so on.
You can also read the CodeWarrior for ColdFire 7.1 installation folder\Help\PDF\IDE_5.9_Automation_Guide.pdf that contains information specific to CodeWarrior IDE automation on a Windows host (see the chapter Command Window Interface and the other chapters describing the IDE automation, command line and scripts usage).
I hope this helps.