Yes, as wasle pointed out, the let's encrypt certificates traefik generates are stored in acme.json by default. If you do not persist this file it will get lost between container re-creations.
The error you are getting is because of not being able to reach your web site from acme servers. It is possible that network connection between outside world and a site running in your VM get disrupted because of the restart. From traefik point of view, there is nothing it can do to help - it's up to you to make sure that the site is up and reachable. If this is not possible you can look at configuring dns challenge instead.