I work with really long video files (anything from 2-6 hours) and when I put one of these clips into the timeline, it will work fine for the first part of the clip but by the end of the clip it will start to lag like crazy. I have gpu exceleration on so I'm not sure why this is happening. It's not high res video either, typically 720
again this only happens when the videos are over 1 hour. If I'm editing a video that's 1 hour long there will not be any lag. If the video is longer, it will start lagging at the 30- 60 min mark.
Editing, Error or problem, Freeze or hang, Performance
Give it a go - test transcode maybe just one long clip on your next edit. Unfortunately with the length of your clips and if you go to something like Prores they are going to be much larger files sizes + the time to transcode. You might get OK results with ProresLT for the Standard Defintions clips.
I would be very interested to hear how you go ... if it does work at least you'll know it's (likely) something to do with the encoding of the original files.