Aperture referencing files to time machine HD instead of from 'working' HD

Every once in a while I will go into a project see the "broken link" icon on my previews. In Finder I check the location I have all my images stored (and initially referenced) on an external HD. They are there.
I go to File>>Locate Referenced Files and see the referenced images have been changed to a location on my separate Time Machine external HD. I locate them and everything is fine but it's annoying.
I don't not have Time Machine on automatic because I have a laptop and like to choose when it backs up. I've looked through other Time Machine/Aperture problems and couldn't find anything. Does any one know of a setting, advice, or have experienced this at all?
Thanks.

Thanks. Sorry, for the delay to answer your questions:
I'm the only one managing the files, and it has happened quite a few times now. The files are in multiple projects ranging from recent imports to projects from a few years ago.
I didn't need to use "File→Relocate Master ..." just the "File→Locate Referenced Files" because my masters are still intact on my working HD. It says that my previous location was on "Volumes/Time Machine/photography/...etc." when I always import masters to "Volumes/My book/photography/...etc"
Does Aperture notice if I move master files because my thought is that Aperture is noticing my TM copying files to another HD and then referencing those instead of my original working HD I import to. Then, the next time I open Aperture it cannot reference the Time Machine files.
Is it because I have TM (USB) backing up my internal HD and my external working HD (FW800)?

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