The lack of interest in this thread indicates me that Fenix5x´s use should be more urban than backcountry / off road. It´s almost impossible to manage waypoints from different locations using only the watch but look Garmin´s answer about it.
"Thank you for contacting Outdoor Product Support. I am happy to help answer any questions you have regarding the Fenix 5x. At this time it appears that removing items from the watch using BaseCamp, is not available. It is not clear if this is by design. However there are no further updates planned for the BaseCamp software. So it is unlikely that this will change. However, in case this is not by design, I have created a research case for our technicians to review this issue. If a change is made for this, you will be reached via email with any further instructions.
In the mean time, you are able to delete items for the watch menu, as well as the internal files while connected to a computer. "
Worst, the have changed the way files are sent from Basecamp to Fenix5x. So instead of separated files they put the new waypoints on top of the older not even allowing the deletion of one batch.