AE CS4 does not support comps over 3 hours.

You should be able to open up your 3 hour comp and split the video layer (Ctrl-Shift-D / Cmd-Opt-D) at the appropriate times, and then precompose each of the split layers into their own compositions. The only problem will be if you would need to output more than 3 hours in one consecutive file from AE. Then you would need an NLE software or probably only QuickTime Pro (but I haven't verified that QT Pro doesn't have a running time limitation, you'll have to do that yourself.)