Greetings!

If you got into command line ftp and left the filesystems read/write, the filesystems would be marked as dirty / needing sync. Unless you were in the middle of something really severe, it should not have caused damage. I have personally FTPed while syncing with emplode. It did not cause any damage.

Can you boot at all and get a prompt? If so, you might want to fsck the drives manually. Also, if you have any preinit software, or if you were FTPing system files at the time (new kernel, init software, etc.), you might want to flash a new version of the kernel in place. Clarification - not the .upgrade, since that requires the disks to be in place to pump the partition. Try one of the hijack kernels, or the base kernel and the logo editor software to flash it.