maybe something for the next SR. If I remove some frames and restart an output than Bongo is checking for missing frames at the output directory. It's a great option, often used here, but it's quite slow, if the scene is complex.
My suggestion - Bongo doesn't go through all frames step by step since the scene update can need some seconds at each frame (recalculating of things like soft edge, meshing, morphing ...). Better it would be it looks for missing frames at the output dir first and than it jumps at the time line to the needed frame.