I don't know, but there is an easy workaround. I'd like to give credit to Dave Pawson for explaining this on his home page. The workaround is to create an exceptions file with the following format:

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You can call this file "pilotSyncExclusions.txt".

You then run pilot-xfer as (for example):

pilot-xfer -e ~/pilotSyncExclusions.txt --sync /shared/pilotSyncDirectory

Note that the -e must come before the backup, sync, or update command that it is modifying.