On several occasions I've had rules disappear. It only happens to rules created with a wizard (switch, drag & drop, etc.), but only if they are not converted to JavaScript, so I routinely convert all rules to JavaScript.
Recently, I had a very complex and time critical job in which I neglected to convert one of my rules to JavaScript, and that rule disappeared between the time I composed my proof file and the time I composed production files. I made no changes in the interim; nor did I close the file or make any other modifications other than settings in the composition dialogs.
Unfortunately, the entire job got printed wrong, and had to be re-printed at substantial cost to my employer.