A few months late but I think I finally found the solution to this annoying issue of Google Drive folders disappearing from Favorites in Finder.
Same like Wazza_Mac and josiahpierce I've found the solution is to change the My Drive syncing options from 'Stream files' to 'Mirror files'.

I can confirm that now it's been 7-8 weeks after I changed the settings on mine, and all my Google Drive folders in Finder Favourites are still there - even after restarts and shut downs :)
I'm guessing with the 'Stream files' option, GDrive constantly purge the offline folders in the Mac, hence why they keep disappearing from Favourites. The 'Mirror files' option takes more space in your Mac as it will mirror everything in your GDrive, but it will solve this issue (and I believe the old Backup & Sync used to default to mirror mode anyway).