@perigalacticon which version of the Arduino core are you using 2.3.0 or later?
I have a very “busy” Windows 8.1 system and bridged routers etc. Invariably I will have 100+ Windows open if you include 4 instances of Chrome. dozens of tabs open in each plus Arduino sketches galore,email etc, etc.
Quite often I find the port doesn’t show in the IDE which then requires a reboot and this can take 10 minutes or more.
I have a much “cleaner” Ubuntu system and that doesn’t have any problem seeing the ports. It could be the different networking protocols between the two OS’.
To be able to see the ports you must have the Bonjour service running on Windows. For my busy system I believe the service simply stops and trying to manually restart it doesn’t help. Bonjour gets installed with printer and networking software but it might be you don’t have it. Check your services.
The other issue when the ports do become available is that you will not be able to do an OTA update until you have unplugged the WeMos as least once since the last flash.
In the newer versions of the core and with verbose compiler messages set there is a message to the effect “numpty you haven’t rebooted since you last flashed”. Even though I am aware of this feature in ESP8266’s I still get caught out from time to time especially as I am reflashing minute by minute through the day.
When you flash via OTA the powering off is not required but during testing a lot of the flashing is via the USB port and hence the feature presents itself. In the real world Espressif are right that when you do a local flash and then take or send the ESP to a location where you are going to use OTA it will have naturally had the required reboot.