Hello,
I have solved this issue by switching to filesystem storage.
You can find the setup for this in the official documentation : joplin/packages/server/README.md at dev · laurent22/joplin · GitHub.
I basically just added STORAGE_DRIVER=Type=Filesystem; Path=/path/to/dir to the environment variables of my docker-compose.yml. You also need to add a docker volume ./data:/path/to/dir to persist the data on server.
I have heavy files in my joplin notebook which, i think, were putting heavy load on the database. With filesystem storage, synchronization seems much faster and no more errors 