Files deleted without my doing anything.

I have hired a programmer to create widgets for my web site. Recently, they disappeared. He has written me the following. Could someone assist me by telling me what I have to do to prevent this from happening in the future. I recall reading something about this problem before, but cannot remember the details. Thank you in advance. Here is what he said:

We have once tried to restore the web site, but it seems you have updated the WordPress files and updated some settings to change the looks of the site and then some files got deleted. However we have uploaded the required files, but it still not working due to some changes in the settings.
After holiday, we will delete the current files and we need to restore the old wordpress settings. Please confirm, we will do that or not?