The installer will never touch any existing data files, this is very important because if we tried to modify them with the installer it would break things. so it's simply not done.
The only explanation I can come up with is that either the files were manually deleted by mistake, deleted during an uninstall (you are prompted to remove them), or they have permission of administrator and your user account doesn't have access to see them.
The last explanation is very possible on windows vista because FlashFXP v3.4 ran in compatibility mode on vista and FlashFXP v3.6 doesn't.
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