From the RAWTheraPee 3.0 Documentation:
If you have saved the above output file next to your raw, you might notice that there's a third file
called DSC_1000.jpg.pp3. This is a little text file that describes exactly what edits you made to your
photo. Just open it in an editor to see how it looks like. Whenever you re-open that raw in
RawTherapee, this file will be read and all the settings from the last session will be restored (the
profile displayed under Postprocessing Profiles will change to 'Last saved'). So you'll never have to
wonder what the sharpening settings were for a certain photo that you edited two weeks ago,
because everything is recorded in this pp3 profile. (To be more precise: nearly everything, as
ranking information is not stored in this file). By default this information is also saved to a cache on
your hard disk (here the ranking info is available indeed). In Preferences, tab Image processing, you
can disable the generating of these pp3 files. But why would you? These pp3's represent all the
work you did on a photo and everybody knows that this can be time-consuming. So keep your
work! You might even want to backup these files, together with the processed photos. In case that
you want to start a new edit session from scratch, simply select the default or neutral profile again.
In essence it is a commonly known as a "sidecar" file, and saves all of your changes separately.