I see that, in fact, the cross repository search currently offered may not be as helpful as the Advanced Search offered per repository (which includes, for instance, the usage of EyeQL, which I think that could be helpful in your case).
I'm afraid I don't have a solution for you to perform the search as you want, but I found some improvement requests on FishEye search that you may vote for, add any comments as you like and also add yourself as watcher, so you can track their progress directly:
You may refer to Atlassian's policy for the implementation of new features.
I thought that the LOC in Fisheye is always limited to the trunk/master? Isn't that the case? I got this information from https://confluence.atlassian.com/display/FISHEYE/About+the+Lines+of+Code+Metric#AbouttheLinesofCodeMetric-LOCinFishEye
I would like to search across all repositories on my Fisheye/Crucible server, but limit the search to the master branch on each. The branches are mostly Git/Stash, but there are some Subversion and Mercurial repos as well.
There are several hundred repos represented, so searching them each individually is not practical.
The goal of this search is to identify the number of unique JBehave stories (files with names *.story). It's a relatively simple search, which Fisheye handles fine, but the results are for all branches, not just master. The workaround I've come to is to search for "*.story" in the main search box. Click the "End" key, then click it again, and again, and again, until I get to the end of the 23,000+ results, and do a text search on the page for the word "master". This gets me close to the number, although it's tough to trust, because some repos or files may have the word "master" in them as well.
In general, it seems that the cross repository search in Fisheye could be greatly improved.