Ok thanks, sounds like I need to fit a switch then (or replace df1 with another Gotek and an identical USB stick). I'd expect a lot are directly probing hardware.
The floppy jumper on the A2000 motherboard does not really "disable" the 2nd floppy, it just blocks the established ID-mechanism for it so the OS will go "2nd floppy-blind".
But all the actual select/motor/data etc lines to the floppy are left intact, so software that just assumes the floppy is there and works at hardware level will still have complete access to the floppy.
If you want to properly toggle the 2nd drive on/off, you must insert an DPST switch inline with the MOTOR and SELECT signals at the drive's connector (this will also block the ID-mechanism).
I guess I could drill one of the blanking plates and fit a toggle there.
I hope by "blanking plates" you mean the metal I/O ones and not the front bezel plastic covers

Even better, one taken from an old ethernet card or similar will already have a usable hole to mount the switch through.