The copy operation seems to have completed overnight without the issues from before. But Putty doesn't keep the full scrollback so I'm not 100 percent certain that it really worked, but I'm going to move forward as if it had worked. At least the tail end of the output looked correct the next morning:

/drive0/fids/18080 -> /drive1/fids/18080
/drive0/fids/18081 -> /drive1/fids/18081
/drive0/fids/180a0 -> /drive1/fids/180a0
/drive0/fids/_00018 -> /drive1/fids/_00018
/drive0/fids/_00018/090 -> /drive1/fids/_00018/090
/drive0/fids/_00018/091 -> /drive1/fids/_00018/091
/drive0/fids/_00018/0a1 -> /drive1/fids/_00018/0a1
/drive0/fids/_00018/0b0 -> /drive1/fids/_00018/0b0
/drive0/fids/_00018/0b1 -> /drive1/fids/_00018/0b1
/drive0/fids/_00018/0c0 -> /drive1/fids/_00018/0c0
/drive0/fids/_00018/0c1 -> /drive1/fids/_00018/0c1
/drive0/fids/_00018/0d0 -> /drive1/fids/_00018/0d0
/drive0/fids/_00018/0d1 -> /drive1/fids/_00018/0d1
/drive0/fids/_00018/0e0 -> /drive1/fids/_00018/0e0
/drive0/fids/_00018/0e1 -> /drive1/fids/_00018/0e1
/drive0/fids/_00018/100 -> /drive1/fids/_00018/100
empeg:/empeg/bin#

I'll also install that pre-release Hijack.