Yes, search for the file "sites.dat" to locate your site information if FlashFXP is not seeing it, and then either use the menu option Sites/Import Sites to bring that file back into FlashFXP or just copy it on top of the file in the Data Folder location.
Unfortunately in Vista, it is not possible for the installer to see files in a users folder and so it can not copy them to the new location. We moved to the new location for the default storage as it is a requirement for Windows Vista Certification.
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