I had a corrupted backup message once, a long time ago. What I have done ever since is use two USB sticks and do a backup to each one every time. They are so inexpensive and a series of them can be rotated if you are over paranoid.
This way, I not only have a second copy, they are not being stored on the same hard drive as the system, or a hard drive at all. I'm also using a small network to USB adapter so that any machine on the network, (the backup 3CX machine), can access the memory sticks.
This is also a good reason to do a backup after every change you make in 3CX, no mater how small, if you don't do a daily backup. If you doing some drastic changes, then do several backups along the way.
Keeping a log of changes, can come in handy too, especially when some problems crop up, seemingly, out of "nowhere". Many issues can be traced back to something that was changed and had an unexpected effect.
I'm not sure if this applies...but make sure that you always use the 3CX Management Console icon, on the local machine, don't go in via a browser.