This appears to still be an issue. Tested using SVN source control, syncing the item updates the hard drive item but not in-editor, leading to conflicts and erased information. this is a fairly critical bug for source control users so im wondering why im still running into it despite finding posts about it from 2015.
Hello Mattk50,
According to one of our developers, fixing this so that you are able to sync to assets that are already loaded in memory is nearly impossible, so it was not touched for an extended period of time. It eventually was closed as Won’t Fix due to a lack of activity. Since you’re mentioning that it still occurs, I can reopen the bug report but I cannot guarantee that it will be fixed.
Edit: In the meantime, I would suggest closing the editor whenever you need to sync any changes to avoid any irregularities when it comes to your data and assets.