Thanks for the reply. We did wonder this, and it's definitely something I could accept as a possiblity, but was is odd is that both includes files were deleted. A mistake could account for one, but it would be very odd for both.
To clarify we are working in the same office, my partner has been doing the majority of the work, but I have changed a bit of CSS, images, etc here and there (nothing complex). In future we could only have one FTP client connected if you think this is a bad idea..
A 'mysterious deletion' of files or folders will not specifically be a result of having multiple FTP clients open at once.
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