I had the same thought as you so I placed Pokemon in the new boxes during an update and nothing happened to them. Unless a big change is made to the box system during an update, you should be fine. Updates do not edit your save files, they only effect the game files such as maps. If you are concerned that you will lose Pokemon, duplicate the file titled 'Box' before every update. It is located in the same folder as the 'Player' file.
If something happens to the Pokemon in the PC during an update, replace the 'Box' file with the copy you made. If that does not work, deposit five of your Pokemon in a PC and save. Copy five of the lines in the copied 'Box' file and move them to file titled 'Party' which is in your save folder. Repeat the process until all of your Pokemon from your copied 'Box' file are back in the PC. I highly doubt that your Pokemon will be deleted during an update but if something does happen this process, though it may be time consuming, should allow you to have backups of your Pokemon in the PC.