No need to remove the drive from the box.
The simplest way (if using non included apps) is to plug the box into a PC via the rear USB 3.0 port and let Windows scan fix any issues caused by changes in Android.
I have often used the network to move/delete/rename files on the internal HDD and it has not caused issues for me. Bulk file transfers I use the rear port as it is a lot faster. Most of my material is on networked NAS's these days, so there are no problems moving files around with these.
Thanks, but I've already have read that solution. I was with the hope the the other I've quoted could be much simpler, if it really works, but wanted to know exactly how to do it.
But what do you mean you have used the network also for deleting files from the internal HDD and had no troubles as such? According these reports it should cause the unused space to be reported incorrectly. Only if the HiMedia's own stock file manager is used for deletion can be this issue avoided. (Which is very odd).
Edit: I would also like to know, if deleting files from an Android torrent client, like tTorrent (installed on the Box) would result the with same issue?