Willmoon,
If you are using or can use MKV files for the merge, MKVTOOLS can do this with no re-encoding.
I have successfully used this a number of times to merge movies that are on multiple disks. Rip the titles using mkv passthu then they can be easily merged together using MKVTools. The program is free and can be found using an internet search.
It will also successfully merge together multiple audio tracks without any audio sync issues.
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