It's a non-issue long-term as flushing will write back to the floppy image in real-time. Until flushing is implemented, the (full) floppy image is only written back when the floppy is dismounted - so a temporary workaround in your case might be to put a blank disc 2 image in the folder and just swap to disc 2 and then back to disc 1 and wait a while before rebooting or powering off.
If you imaged as a JFDm make sure your disc 1 floppy image is not write-protected and had the "Flush" flag set when you initially imaged it (just reimage if you're not sure). As this game doesn't use any complex protection, you can speed things up by imaging as an ADF.
The protection is multi-layered, with BASIC intermixed at various stages, so it's not possible to live-patch the individual games. At least three of the BASIC files have "$.x" hardcoded throughout it, so it's expecting to read/write from the root of the current filesystem.
There's no virtual environment on the machine you're playing it on, ADFFS is just acting as a floppy emulator. It's only on RiscPC and later that virtual environments come into effect when the JIT is used.