Guild Wars 2

Today before the daily reset I somehow lost 31 quartz crystals that were in my inventory the previous night.

No biggie, I bought 25 and transformed them into a charged quartz. This was my first transformation for a charged quartz so I only had one.

I then left for a few hours and came back after the daily reset to do dailies. I then noticed my charged quartz was gone!?

Thanks!

Have you checked your collections tab in your bank?

Indeed, it sounds like you hit Deposit Collectibles at some point. Regular Quartz goes into the jewels section, while Charged Quartz is in the rare materials section.