First of all, if you have a desired fixed target file size then this manual bitrate tweaking method is just a waste of time, IMHO. Reason is, you cannot raise the global average bitrate in this case. So as you walk through the GOPs and raise the bitrate for individual ones, CCE will have to take bitrate away elsewhere to satisfy your request to raise this GOP's bitrate. IOW, if you had managed to complete this process and finally walked through the graph all the way back, you'd been shocked to see that it turned back grey or even red in many, many places. So maybe you should be thankful that it crashed quite early
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CCE is really the master of VBR and especially if the average bitrate is low, I suggest you simply do a standard 3 pass VBR and I can almost assure you that the result will be very good.
As for why it crashed anyway, there can be many reasons. This operation is very sensitive to bad memory, make sure your system is not overclocked and your memory sticks aren't faulty. Also what version of CCE are you using?
In any event, as soon as CCE displays "Clean" in the upper right of that dialog, your modifications are saved to the VAF. Have you tried to just reopen the project to see if your modifications are still there? They should unless the crash trashed the VAF file.