Decimating Non-Uniform large time-series data
I probably wouldn't bother interpolating at all. You want to downsample by factor 128 anyway, so from that point of view, your raw data is already a good approximation of being uniformly sampled at 128Hz. Just go with low pass filtering and downsampling and you should be good. Try it on a small fraction of the data, to get an idea of the error you introduce by this approximation, my gut feeling says, it will be acceptable, i.e. small compared to the accelerometer error. If actual time span does matter, calculate the average sampling rate and use this value instead of 128Hz.

For handling large data sets with limited RAM, I would opt for generators in python (yield instead of return) This way, there is no need to keep all the data in memory, you just "stream" the data from file to file in (overlapping and  windowed) chunks of appropriate size.