This can be done.
there are two ways
1. this first method provides more control as you can enter a specific path. create a windows shortcut and set the "start in" folder to point to a new location which contains your data files, they must exist prior to starting FlashFXP if the flashfxp.ini is not found it will automatically default to the folder with the flashfxp.exe
2. This requires one of the latest betas. Start regedit.exe and add the following key.
[HKEY_LOCAL_MACHINE\SOFTWARE\FlashFXP]
"APPDATA"=dword:00000001
When this key exists FlashFXP will use the application data folder to store site details. Which is usually "C:\Documents and Settings\<user>\Application Data\FlashFXP"
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