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

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.

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.

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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.

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^{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();