I am not sure what you mean by "Safely" - are you referring to the potential downstream effects when you sync up to your PC. Is this the only device that has the project on it or are there other devices (SPS or Machines) on the same project that will need the data after you have deleted it, or is the project completed and no longer needed by anyone, or was it a Test Project that noone ever used - you just created it for testing / learning processes. Depending on your answers to the above will dictate the safest way to do what you are trying to do.
As a general rule - if this device is finished on the project but the project is ongoing - then I would use TBC / SCS Data Manager to take the device off the Project first (you do that through the Job Site Manager and reassign Controllers and deselect this device - that way it is disassociated with the Project so any changes you make on the device for that project will not affect anyone else.
Now you should just be able to use File Explorer and remove the project from the Trimble Synchronizer Data folder on the device - I would most likely first move it to a Backup Location rather than delete it (e.g. make a \Documents\Backup Projects folder and move it there first) and make sure that by doing that you are not screwing anyone else up on site through a sync process
If you are using Office Synchronizer on the device to Sync to a USB Stick and then using the USB Stick to Sync with the office PC or if you are Synchronizing through TCC will also have an impact on how you should manage this process.
If on the device you remove the Site Folder from the synchronizer data folder then when you sync up next time it will remove it from the Device Folder on TCC and from the Office Computer. Same in reverse - if you unassign the controller from the project then the Project Folder and all Designs and Work Orders will instantly be deleted from the Sync Folder, and on next sync to TCC and the Device they will be removed automatically - so typically I would
1) Synchronize Fully (Device to TCC or USB Stick and TCC / USB Stick to the office computer - to make sure that all the Controller Data was on the Back Office Computer
2) Make a Backup Copy of the Device / Project Folder on the Office PC so you have everything backed up before you start deleting / reassigning things
3) Unassign the controller from the project using Jobsite Manager in TBC / Data Manager
4) Sync Up again from Office PC to TCC or USB Stick using Office Synchronizer and then again to the Device and that will remove the Project Data and all Designs and Work Orders for that Project from the device
Hope that this answers the question
Alan