Let's face it, developers are not going to remember to select "Leave existing estimate of" every time. They will use the default, "Auto adjust", no matter what you say they should use, because they will forget.

As long as the "Total Time Spent" (TTS) is less than the original estimate, you can reconstruct the original estimate by adding the TTS and "Estimated Time Remaining" (ETR). But as soon as you log more time than you originally estimated, the ETR becomes fixed at 0, and the original estimate is lost entirely. This means you lose all track of your original estimate at the time when you need it most, when you've gone over.

I can see three ways to fix this:
1. Allow the ETR to go negative.
2. Change the default to "Leave existing estimate of".
3. Allow the system administrator to configure the default.

The first two options would be quite simple; the third would require some design.

(In case I haven't mentioned it recently, I really think this is a great product, despite my specific complaints.)