Bad news. After doing some testing I've asserted that it's impossible to copy paste the inputs in order to get the new segment. At first, I thought that I had desync'd but after some further testing (going as much as -2, -1, 1 and 2 frames) I decided to juxtapose two moments 300 frames into the room where things were going off the rails and I got this:
Seems like the problem is the enemy rng has completely changed, despite every action being exactly the same save for the actual boss fight. Unless there is some way to copy paste the rng values, I don't think this method will work.
I would like to hear some suggestions but I have currently a plan if all fails. It's not what I'd like, as it will not be the proper way of doing things but I think it might work for the intended purpose.
I have already registered the frame count difference between the newly recorded fight and the previous one. I will do the same with one I still have to record. I can then add the values of the both frame counts so I can find out how many more additional (or most likely subtractive) frames it has. Afterwards, I will make another recording where I clear all the enemies and make another count. Let's say that there a total less 2000 frames from the newly recorded boss fights and the part where I clear all the enemies and return is 3000 frames. I can then, in the original movie file, skip clearing all the enemies and return in exactly 1000 frames (gaining the 2000 frames from the boss fights by not clearing all the enemies) so that the timer aligns to the expected time from the new boss fights. Unfortunately this means that I need 4 different files (the original file, the file with new boss fight 1 & 2 and the file where I clear all the enemies) and will need to break apart the whole thing into 7 different appends before creating the finished video (I fear keyframes in VirtualDub might make my work harder but if it's anything like FRAPs encoding it should be fine since every frame is a keyframe - I imagine this is where the codec chosen comes into play).
What do you guys think?