HandBrake

I'm struggling to a bluray ISO which had multiple clips in to one video file. Iv added them in to makemkv which then creates individual mkv files, iv then tried to add all those files to handbrake but it only scans and allows for one file. I tried a program to merge those files together with little success. Any pointer in what I want to do?

For merging BD titles I've had a lot of success with MKVToolNix - simply "add" the first file, then "append" the additional files before selecting your output file and muxing.

That's the one I'm using, keep getting error saying uid is being used for output.
Will try again to give exactly what it says.
Could you give me an idea of the process you use to add the files as I just selected them all and dragged them in

Really struggling to get this to work, I've tried adding the first file then append files after but no joy

You have to add them one at a time... bulk drag and drop won't work AFAIK.