P . Weber 

I would disable autopropagation and do two things:

1. pre-translate before you start work each day
2. not worry about having the autopropagated result since I probably still need to check and confirm it when I get to it

The excessive time it's taking to AP because you have a large file doesn't get you the benefit you're looking for, so change your approach with a file like this and just deal with the new 100% match when you get there during an interactive translation.

Another approach, given it seems to be alphanumerics mainly is to filter on these segments now, then copy source to target, change status to confirmed and clear your filter.  Now that won't affect your workflow anymore. It's often a good idea to take advantage of the filtering possibilities and tackle large chunks of content quickly in one go... if the content allows you this time saving process.

P . Weber 

Please check your autopropagation settings. If you do NOT confirm autopropagated segments, the AP process will run for the same content on and on again until you reach the last item in the row. This makes no sense in such a huge file. So what you should to is set your AP as follows:

Other, maybe much better way to deal with such huge file, would be exporting unknown segments in first step. To do that, chose the batch Analyse and in the settings chose this:

Then translate this much smaller file and use the resulting TM to pretranslate the big one. In the end you should have only few or even no segments to translate in the big file.