If you're referring to the top ("replay") timeline, then that's a bug. The theoretical limit for replays is somewhere around 31 days which should be plenty.
If you're referring to the bottom ("video") timeline, then you're misunderstanding how it works and should read up on time keyframes.
"By the way, thanks for such a quick responding, this is really awesome."
Uhm, I'm sorry in advance, since I've now got all the input I need, I'll now be putting this on my todo pile and that pile has grown quite a bit since the last time I worked on it.
Based on the fact that there's a raw file and that the raw file is larger than the other one, I'm guessing this is an issue with the Replay Editor (which is also powering the start/stop/pause/resume recording feature).
If that's the case, then you should be able to just use the file from the raw folder instead (by just moving it one folder up). It won't have the start/stop/pause/resume changes applied but it'll at least be complete.