I found a hard fought solution. I will provide some explanation to prove why this solution is necessary, but it ends up being relatively easy to implement.
A big part of the problem is that when you stop USB and de-initialize the core, you still do not have control over the pin. You can try to make it an output and drain the pin low and you will not be able to because the FS core remains in control. In order to do such a thing, you need to toggle the GCCFG bit after deinitializing the FS core, which is not done automatically in the HAL deinitialize function. This can be done as follows
USB_OTG_FS->GCCFG &= ~(USB_OTG_GCCFG_PWRDWN);
Once you have done this, you can then reconfigure the pin as a GPIO push pull output and set it low. This will force the line low, causing your host to finally see a disconnect. Re-initializing the USB will then tell the host to re-enumerate the device.
