I have found out, if I save to and different file name each time I don't have this problem. The only time I had this problem if I save to the same file by click the save button on top instead of using the save as. It seem to me that is when it saves to the same file it over writes the file and deletes the old. I don't known.
At first I thought you sere talking about having "some" of the sheets [in a multi-sheet draft] disappear within a single draft file.
Now, it sounds like you were expecting the system to know the content of a drawing is different to an existing one, when saving to an already used name.....if the "file" has the same name of an "existing" one, then Windows will "overwrite" that one, with the new one. That is an expected outcome of almost every application I have encountered.
The easiest way to stop this, even accidentally, happening, is, in Windows Explorer, right click for the file properties, and mark the existing file as "Read-only"....the operating system will then force you to save as a different name.