With all that footage here’s what I’d do.
Calculate the number of frames you want to end up with (final frame rate x final run time for the time lapse). Then divide the footage by that number, then by the time of the raw footage. So you end up with something like 1 frame per 60min or whatever. Then I would make a batch script for FFMPEG to save out single frames based on that time for each large video file – like for a two hour video, save out a frame every 60 min. giving you two frames. Then use whatever your NLE is to compile all the frames into a single video – that’s the timelapse.