The very fact that when you move the topics up a few levels strongly would make you think that the problem is the length of the path name, either in itself or because it causes text wrap.
However, the example you quote in  is not that long and I know I have some that are longer.
I wonder if is time make a copy and then trash the CPD file?
See my site - Opening Projects.
If that does not help, still leave the back alone and in the working copy try shortening some paths. RH does the rebuilding of the links so you just have to rename the folders.
Kathy, a thought--
Did you create all these folder, subfolders, subsubfolders entirely within the RoboHelp project manager, (rather than in Windows directories) and move the topics only in RH explorer?
If so, I'd go with Peter's suggestion. Your links might be breaking a field-length limit in MS Access.
Another observation is that folder names in RH do not have to be the same as their TOC entries. For example, Back Office Administration in the TOC can refer to a folder named BackAdmin.
I know this topic is old news but after searching and searching I found that the problem you experienced was the same one I was having. I decided to rename, by shortening, the topic that I was having problems with and wha-la the broken link finally disappeared. I believe, as you do, that it might have something to do with linking to a topic at another level which might be creating a lengthy path name creating the broken link. I tried moving the topic up a level and that did not solve my problem but renaming did. Just thought I'd share this information for anyone else running across this problem.
In addition, the path that was presented in step 4:
<a href="../../../Back_Office_Administration/Setting_Up_Locations/Understanding_Locations.ht m">Understanding
could certainly be shortened to:
<a href="../Setting_Up_Locations/Understanding_Locations.htm">Understanding Locations</a>