Where/how does RH update an .hhp file?

We've been having a recurring problem where compiling the master .chm in our group of help files somehow overwrites the correct paths in the [MERGE FILES] section of the master's .hhp file with incorrect paths.

Since the paths point to a "Recovery" copy of our help file from an apparent crash (pre-dates me), my original assumption is that, somehow, either a crash or user-error has resulted in incorrect links being buried somewhere in the main project that causes this phenomenon. So far, I've been unable to track down a source.

After posting and reading similar topics, I found a solution in compiling the main, correcting the now wrong .hhp, and recompiling. It works, but why exactly the .hhp is overwritten the first time but not the second is beyond my level of comprehension (I assume some sort of change activity triggers RH's desire to overwrite, but I haven't found the culprit).

Regardless, can anyone tell me exactly what or where in RH this overwrite action is triggered? Or at least what action(s) cause RH to think the .hhp file needs to be overwritten? Given the nature of the link it's trying to point at, my assumption remains that this is somehow still related to the aforementioned crash, and that somehow an incorrect set of paths has been saved somewhere and, for whatever reason, RH thinks these are the right paths and overwrites what's in the existing .hhp file.

When I started here, we were on RH5, but have recently upgraded and moved our help files to RH7. I've also deleted the Recovery copy that the .hhp file gets re-pointed to. Neither has altered this behavior.