Every time you start syncing a folder with Boxifier, you see a check box that allows you to protect that folder. But what does it mean exactly?
When you mark a folder as protected, deletes and updates made from other devices linked with your Dropbox account or from Dropbox.com will be rejected by Boxifier when synced down to that folder. This way, if you accidentally delete a file from a protected folder using Dropbox.com, when that delete will be synced down to the folder, Boxifier will see that the folder is a protected one so it will reject the deletion and the file will re-appear in your Dropbox account.
This feature protects your folders only against updates and deletes made from other devices linked with your Dropbox account or from Dropbox.com. Any deletes and updates that you make from the computer where Boxifier is running will be synced to your Dropbox account even if the folder is marked as protected. It is only deletes and updates made from other computers linked to that Dropbox account that are rejected.