I've found the answer in the package documentation. This solves the problem I had, where the computer initialising the tracker was in a different timezone (London), to the participant using the tracker (Nairobi). The resulting output using the code below showed the correct hours of waking/sleeping in the summary CSV

Overwrite = TRUE was required to reprocess the input files.

Please remember that stating the different times zones (as in the code below) will change the config file, which will keep these settings until you reset or change them. It's probably easiest to move to a different output folder for trackers in different time zones. This should revert to default settings.

GGIR(datadir="/my/path/input", 
     outputdir="/my/path/output",
     studyname = "My Study",
     overwrite = TRUE,
     desiredtz = "Africa/Nairobi",
     configtz = "Europe/London")