First, make sure the actual files are still in the Data20 folder (Or whatever folder you store all your client files in).

In my experience when it says Delete Record in HB, that means the file is missing from the folder that its looking at, so its going to remove the file listings in the HB to match whats actually there.

Maybe some files got saved to a different folder somehow, so they werent found in the default folder that HB Maintenance looked at.