Judging by the github issue list there are a lot more issues with Docker.qcow2 now than before. Mostly related to Docker.qcow2 preventing docker from starting.
Looks like a bad release. Hopefully 1.13.1 is soon.
There was a race condition in a previous release which could allow multiple hypervisor instances to open the Docker.qcow2 simultaneously. Unfortunately this can corrupt the file by allocating the same physical block (cluster) twice, resulting in bad things happening. When this file-locking bug was fixed we also added an integrity check which checks the structure of the Docker.qcow2 on every application launch. For safety the app refuses to start if corruption is detected.
I believe that in these cases, the corruption happened in the past and is now being detected since the upgrade. Unfortunately if the app refuses to start it makes it difficult to reach the "Reset to Factory defaults" menu option. The workaround described here https://github.com/docker/for-mac/issues/1159#issuecomment-2... is to remove the qcow2 and restart the app. Unfortunately containers and images will need to be rebuilt.
For what it's worth after the integrity check and the locking fix went in, I've not seen any recurrence of this error. Please open an issue if you see any other problems!
Looks like a bad release. Hopefully 1.13.1 is soon.