For playbackability with VDR in the 'simplest' case you only need to fix the file-number in the index.vdr-file and append that onto the first recording and move the XXX.VDR-files with the fixed name into the first recording dir.
But that way the overlapp would still be there.
So you needed a program that finds the exact frame where the first recording stopped. Then finds the exact same frame in the next recording and then copies the portion of 001.vdr from the next-recording and appends and fixes the content of the index.vdr beginning after the frame you
A bit simpler:
1. Move all the nnn.vdr files into new directories, renumbering them in the right order and make sure that each possible overlap is actually in one dir. E.g. if you have 1/001-1/005, 2/001-2/255, 3/001-3/023 you could reorder this as x1/001-x1/004 (from 1/001-1/004) x2/001-x2/099 (from 1/005, 2/001-2/098) x3/001-x3/178 (from 2/100-2/255, 3/001-3/023) (You can completely disregard index and other files.)
2. Run genindex in each of the new dirs.
3. Fix the cut-points. This is left as the only programming exercise, but supposedly noad can do this already (-o flag).
4. Run vdrsync --cut or whatever.
I'm doing this routinely (by hand, don't ask me for a script :-) to join multi-part episodes of certain shows. Here the first step is trivial as most recordings consist only of 2 or 3 nnn.vdr files and for the third step I need noad anyway.
Olaf