There seem to be some bugs that still cause this to happen. I just had the same thing happen with a database I have been using for quite some time. I thought it might have been related to a fragmented file after a number of adds/deletes, etc. so after a significant amount of use I would execute the sql command -shutdown compact-. That seemed to make things a little more stable and reliable until I encountered the same problem after just one simple record deletion. There just doesn't seem to be a way to ensure data safety. This is a very bad problem when you expect to have a reliable way to store information.
I am using version 3.5.5.3 and am reluctant to try 3.6 since there have been some Base stability reports for that version as well.
Sorry, but I cannot offer any solutions. I would like to file a bug report but cannot get any kind of a handle of how or when this problem pops up. I have resorted to making frequent file backups and hoping for the best.
Where did you save the file? In a pen?. Also remember that Base it's a embedded database, only when you do the save, the data is written to disk.