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How do I set in and out markers in order to encode only a segement of a file?

Hybrid has an *experimental* cut option which probably allows what you want.
You can enable it under "Config->Internals->Cut support *experimental*", make sure to read the tool-tips thoroughly and remember this is an experimental option. (Might not always work as intended/hoped, especially on non-file input for with vfr content.)

Cu Selur