This week's book giveaway is in the OCMJEA forum. We're giving away four copies of OCM Java EE 6 Enterprise Architect Exam Guide and have Paul Allen & Joseph Bambara on-line! See this thread for details.
Well to start off with you'll want to look at the File I/O tutorial which will quickly guide you on how to read in data from a file and write data to a file (including line by line etc).
Depending on your memory/performance limitations I'd be tempted to read in the properties file and store the key/value pairs in a Map. Whether you try to replace the keys in the actual file 'on the fly' (more difficult) or write out a new file (easier but you'll need to rename the original file etc) is then up to you.