That's what I think I'll do. But how do I prevent the problem from happening again?
You should make sure that you always have at least 2 copies of your music.
Take the SDCard out of the Pono and put it into a USB SDCard reader and use the windows file Explorer to copy the files to a backup location (like to your PC Music directory).
If you have files on the internal Pono drive you'll have to connect the Pono via USB and it will show up both in MC and also as removable drive(s) under Explorer.
You can use Explorer again to copy those from the removable drive(s) to a backup location.
The Pono is deadly slow copying files using a USB cable to it.
It was never fast but somewhere in the last firmware updates they really messed it up.
I don't bother with the internal drive, I put everything on a SDCard and use MC to treat it as a handheld copying files from the Music directory on my PC. That's as fast as your SDCard and computer can go. In my case REALLY fast.
The reason I use MC to copy the files to the SDCard and not just explorer is that I have some music that the Pono can't play natively so I setup the SDCard as a handheld in MC with the proper conversion parameters. If all of your tracks are playable by the Pono you could just use Explorer to move them onto the Pono.
I have a 400GB SDCard for my Pono with all of my Music on it (and the PC too and also on a PC backup).
When you fill one of those from scratch it takes the Pono a couple of hours to index it when you first turn it on