There has been another update since then so that makes sense. Your server most likely isn’t missing, it could be that your instances.json was corrupted somehow or something else might’ve happened.
Take a look through this guide here to ensure that your instances.json file is all safe and sound, then check the filesystem to see if your server files are there.
If that all looks fine and good, take a look through your deployment log to see if there’s anything weird there.