I ran into the database corruption a while back and my workaround is to reboot my Kobo Sage before connecting to my computer. I use a menu item in NickelMenu to do this. I can do the second connection to send the metadata for newly added books without needing a reboot but any time I've been reading, the reboot keeps me from seeing database corruption.
You may want to take a look at the
Firmware 4.38.21908 thread in the Kobo forum for more discussion.
Kobo is aware of the issue and it should to be fixed in the next release.