I use Microsoft Synctoy to sync two calibre library folders on two different computers.
I run Sync toy on computer A to backup my library to my portable harddrive (After losing my library when my computer crashed i now keep a backup)
I then go to computer B and run synctoy on the library folder there which transfers all of the changes between the two folders. This has the advantage that any change to metadata or book covers transfers to the library as well.
As of yet i have had no problems and issues to report on this method. However i do the sync before opening Calibre on Computer B. I suspect that if i was to work independantly on each computer it would fall down and the way sync toy works is to replace the older file with the newer file. which means that the Calibre database file will only copy one way losing all of the data on either Computer B or the portable hard drive.
The solution i use is to only ever work with one Computer at a time e.g. wirk on Computer B. Backup and sync with Computer A prior to working on Computer A. It may seem a complex way of doing things but i work on multiple computers via backups and this way of working is second nature to me.