Connecting to the scope object in Python doesn’t configure the clock; you can use scope.default_setup() to get our default settings (including the clock).
You should (almost!) never have to re-connect the USB cable for normal use.
Typically, the cause for this is that you have the scope still connected in a notebook somewhere, and are trying to connect to the same scope in a different notebook. In the first notebook, either run scope.dis(), or re-start the notebook, to avoid this. (this is explained here)
LEDs are documented at the top of the RTFM page (visually).
Normally, the blue “USB enumerated” and green “FPGA heartbeat” LEDs blink in a steady pattern to indicate that “we’re alive”.
scope.dis() did the job, and you were right - there were more scope connections open.
I saw that one, but I was looking for a table with detailed steady/flashing explanations. I thought I’d missed. Never mind … the picture does the job as well …