The command line option '-datafolder' is an override the registry. Currently it's not possible to single out the sites.dat file from the rest of the data files.
If you don't intend on users modifying the sites.dat, you could write a batch file or script to copy the sites.dat to the FlashFXP data folder prior to starting FlashFXP. That way each user has the latest sites.dat when they start FlashFXP.
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