Flash should restore everything, partition repair via re-install won’t be an issue. The trick is that when you use a virtual machine as your flash host there are a lot of little details which can get in the way (as compared to a dedicated flash host). I suspect all of the issues you are having is because of this.
I don’t know the exact nature of your virtual machine setup, but there are often two places where this goes bad. The first one is that your virtual machine may not be where the USB port for recovery mode is routed…even if windows can see the port, the virtual machine may not; and in fact, if windows sees the USB device, probably the virtual machine can’t. Under Linux on a command line prompt, this command will be empty and show nothing if the Linux install can’t see the device (the JTX1 must be in recovery mode as well, simply connecting it with power on won’t show recovery):
lsusb -d 0955:7721
Recovery mode is reached if the recovery button is held down at the moment of power up or power reset. The button does not need to be held down for any significant time, e.g., hold recovery and simply tap the reset button and let go.
A second part of a common virtual host flash “gotcha” is that the file system underneath the Linux install MUST be a native Linux file system type, e.g., ext4. Type NTFS cannot work. Also, the Linux partition must have a lot of extra room for creation of the loopback image and/or sparse version. Having an extra 35GB would not be overkill.