Ohloh now sees only one create commit, but two delete commits. This leads to negative line counts.
Oh dear, this sounds completely familiar to me :)
I wrote a tool years ago called cvsmonitor (that FishEye later "cloned" and made much better).
I had a fundamental bad assumption in my math that could be described as the following.
"The line total at a desired point in time is equal to the known line totals at a given point, plus the sum of the deltas between the known time and the desired time"
This works just fine on the trunk, but leaves you in a quandary of two choices.
EITHER
a) Track "line total over time" for only the trunk, ignoring all work occuring on branches.
b) Track "line total over time" including the branches but have incorrect totals.
Most people choose b) because it gives maximum credit for work done, and if it artificially inflates the apparent size of a project, well then most people are happy to quietly turn a blind eye.
It only really gets noticed when the totals go blatantly out of sync, or during branched deletes.
The solution, really, is that you need to track contributions, rates of change and total change DIFFERENTLY to the running line totals, because in a situation with multiple timelines the two unhook from each other.
You keep tracking change over time on branches and crediting them to contributors, but you derive the project line totals over time ONLY from the subset of changesets that occur on the trunk.