A good safety feature would be a prompt, "Do you really want save-as to  a temporary directory?" But I guess the difficulty there is that the save-as is being done from within Word.

The problem would be fixed if (1) TheBat could place the file in a permanent directory or the users preset choice instead of a temporary one. In my case the folder being used is one that belongs to TheBat!: C:\Users\...\AppData\Local\Temp\Bat.  So it seems that TheBat could simply use another, user-specified directory for this, and not flush it.

Or (2) ... there could be a choice for TheBat not to flush the temp directory at all, leaving that for the user to do manually.

Or (3) ... TheBat could use a Backup subdirectory in the temporary folder, and on each restart  flush that folder and then refill it with a Move of any files in the main temporary folder. That way a user might have some chance to recover work that otherwise would be lost.

In virtually all cases when I have this problem, I have done a save-as but didn't realize that was being made to a temporary directory.  In all of my other workflow, I have the programs setup to do Save-As ops to my workspace folder; TheBat is the oddball that doesn't do that, and problems result.