1. I noticed that after a wu completes, boinc uploads the 'result' file immediately but sometimes leaves the 'workunit' file behind. Are the work units officially done when the result file is uploaded or after the workunit has been removed from my project folder?

2. When I upgrade boinc, can I just replace the single boinc application file or is it better to clear the whole boinc directory and start fresh?

1. The work is officially done when the file is uploaded and the scheduler is queried the next time. I think this is also the moment in which the completed work unit is deleted. Note that you don't necessarily get credit at this time.

2. I always only replaced the BOINC executable and never had any problems.

fabian