Well, 

the problem was solved at the end, please don't bother answering. 

Following the advise of one of the Orca developers, Christoph, I changed
QMMMscheme to normal instead of ONIOM and disabled periodic boundary
conditions.

Now the files are extracted normally.

for further reference, one should get in the working directory these files,
important for the calculation:
basename.LJ
basename.LJ.excl
basename.pc
basename.pcgrad

M.

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