Are the boxes 2 upgraded V6 boxes so they both have hard drives. If that's the case and the recordings that have disappeared are all on one box so there are no recordings left on that box and all the recordings you have left are on the other box. Then you probably do have a faulty box.
You could try doing a factory reset and if you have no recordings select the option to format the hard drive, you will have to sign into your apps such as iPlayer, Prime, Netflix and ITVX again, also Match frame rate and Standby power consumption will go back to their default settings if you have changed them.
If it does it again you can either call Virgin on 150 from a Virgin phone, mobile or landline, or 0345 454 1111 from any other phone to report a fault or come back here for one of the forum team team to pick this up which might be 2 to 3 day's.
If you do have 2 boxes with hard drives and have one replaced there is a good chance it will be replaced with a 360 mini box with no hard drive.