How to overwrite one property in .properties without overwriting the whole file?

The Properties API doesn't provide any methods for adding/replacing/removing a property in the properties file. The model that the API supports is to load all of the properties from a file, make changes to the in-memory Properties object, and then store all of the properties to a file (the same one or a different one).

But the Properties API is not unusual in the respect. In reality, in-place updating of a text file is difficult to implement without rewriting the entire file. This difficulty is a direct consequence of the way that files / file systems are implemented by a modern operating system.

If you really need to do incremental updates, then you need to use some kind of database to hold the properties, not a ".properties" file.

Other Answers have suggested the following approach in various guises:

1. Load properties from file into Properties object.
2. Update Properties object.
3. Save Properties object on top of existing file.

This works for some use-cases. However the load / save is liable to reorder the properties, remove embedded comments and white space. These things may matter¹.

The other point is that this involves rewriting the entire properties file, which the OP is explicitly trying² to avoid.

^{1 - If the API is used as the designers intended, property order, embedded comments, and so on wouldn't matter. But lets assume that the OP is doing this for "pragmatic reasons".
2 - Not that it is practical to avoid this; see earlier.}

You can use PropertiesConfiguration from Apache Commons Configuration.

In version 1.X:

PropertiesConfiguration config = new PropertiesConfiguration("file.properties");
config.setProperty("somekey", "somevalue");
config.save();

From version 2.0:

Parameters params = new Parameters();
FileBasedConfigurationBuilder<FileBasedConfiguration> builder =
    new FileBasedConfigurationBuilder<FileBasedConfiguration>(PropertiesConfiguration.class)
    .configure(params.properties()
        .setFileName("file.properties"));
Configuration config = builder.getConfiguration();
config.setProperty("somekey", "somevalue");
builder.save();

Properties files are an easy way to provide configuration for an application, but not necessarily a good way to do programmatic, user-specific customization, for just the reason that you've found.

For that, I'd use the Preferences API.

I do the following method:-

1. Read the file and load the properties object
2. Update or add new properties by using ".setProperty" method. (setProperty method is better than .put method as it can be used for inserting as well as updating the property object)
3. Write the property object back to file to keep the file in sync with the change.