My way around this was to deactivate the display time-out during sync. That should be possible on most Android phones. Depending on your connection it shouldnt take hours.

I didnt mean the sync between source machine and the Linux machine. I meant the sync with the mobile device. In the app settings you can view your "sync status", on the desktop as well (in the menu "help"). It should look like this:
image
Is it the same between the desktop and mobile? From my experience Joplin will download all files and resources first. Your folders will only show up at the very end of the sync, so it looks like nothing is happening.

Moreover the error log of your mobile device would be helpful. Perhaps it shows whats going wrong.

Personally I dont think that 400MB is that much data. My database used to be bigger and I had not problems syncing with OneDrive on multiple devices. And import is one of those things that breaks sync targets quite easily, so it can do more harm than good.