You can specify a new data location in the windows shortcut by changing the startup folder. Provided you didn't select the "Per-user settings" during install, if you did see the text below.
You will need to place the flashfxp.ini into the data folder before FlashFXP will accept this new location.
Using this shortcut method is not an ideal solution, I had intended to add a specific registry setting, perhaps I'll add this into the next beta. It's been on the to-do list for over a year now.
Disabling per-user settings
During installtion you selected to use seperate settings for each user account "Application Data Folder" because of this there is no way to override the location of the data files are stored.
To allow storing the data files anywhere you're going to need to undo this setting, however you wont be able to keep settings per-user.
You need to set the follow registry key to disable this option.
[HKEY_LOCAL_MACHINE\SOFTWARE\FlashFXP]
"APPDATA"=dword:00000000
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