One special feature of Boxifier is that when syncing folders with Boxifier you don't have to worry about wasting space on your computer.
Boxifier synchronizes outside folders with your Dropbox account without those folders taking space in the local Dropbox folder on the computer where Boxifier is used. That means, the folders that you sync with Boxifier are synced directly to your Dropbox account and accessible on www.dropbox.com and other devices where you use Dropbox. In order to save space they are not copied/downloaded to the Dropbox folder of the computer where Boxifier is being used to sync them.
However, if you navigate to the Dropbox folder on the computer where Boxifier is syncing those folders, you will find that Boxifier creates shortcut files corresponding to the folders that you are syncing with Boxifier.
Why does Boxifier create shortcuts?
Boxifier does not use shortcuts to sync outside folders with Dropbox. The only reason Boxifier creates shortcuts is to give a visual reminder to the user that folders are being synced in those locations of the Dropbox account, even though they are not wasting space on that computer. Shortcuts are not relevant to the syncing process, but they are a convenient way for the user to jump to the original location of the folders being synced. Shortcuts are there just to guide the user and are present only on the computer where Boxifier is used to sync those folders.
Please note that the actual contents of the folders are being synced with Dropbox, not the shortcuts, as can be seen by checking the Dropbox website or any other device using Dropbox. Checking the corresponding locations reveals no shortcuts, only the contents of the actual folders being synced by Boxifier.
The folders you sync are not copied to the local Dropbox folder, they are synced directly to your Dropbox account and can be accessed via the Dropbox website and other devices using Dropbox.
If you access data synced from a network drive/share/NAS or server and you want to have a local copy of the folders from the network drive/share/NAS or server, you can have it by using the Offline Folders feature. In order to use it, open Windows Explorer and navigate to the folder on the network drive, right-click on it and then click the "Always Available Offline" menu option.