eac3to is able to convert E-AC3 and TrueHD audio tracks to AC3 or FLAC eac3to is able to convert E-AC3 and TrueHD audio tracks to AC3 or FLAC.

TrueHD conversion unfortunately doesn't work with demuxed TrueHD files at this point in time. The to-be-converted TrueHD track must the first (or better: only) audio track in an EVO file. Please use the EvoDemux tool to create one EVO file for a full movie with only the TrueHD audio track in it.

Usage: eac3to src.eac3|evo|wav dst.ac3|flac|raw|wav [-options]

This tool can convert a 2.0 or 5.1 E-AC3 or a 5.1 TrueHD track to AC3/FLAC.

Options:
-192 use 192 kbit/s for AC3 encoding
-448 use 448 kbit/s for AC3 encoding
-640 use 640 kbit/s for AC3 encoding
-orbitlee force the use of Orbit Lee's DD+ source filter
-nero force the use of Nero's filters
-keep24 don't convert TrueHD output to 16 bit
-96000 TrueHD output is 96 kHz

Supported source files are:
(1) demuxed E-AC3 audio file, 2.0 or 5.1 channels
(2) EVO file with one 5.1 E-AC3 or TrueHD track in it

For converting a demuxed E-AC3 file you need these filters to be installed:
(1) "Sonic HD Demuxer", "Nero File Source / Splitter" or "DTS/DD+/AC3 source"
(2) "Sonic Audio Decoder 4.2" or "Nero Audio Decoder 2"
(3) "Dump" filter

For converting an EVO audio track you need these filters to be installed:
(1) Nero HD-DVD/Blu-Ray plugin
(2) "Nero Splitter"
(3) "Nero Audio Decoder 2"
(4) "Dump" filter

Furthermore these tools must be located in the same folder as eac3to:
(1) sox.exe - version 13 or newer
(2) aften.exe - revision 449 or newer
(3) flac.exe - version 1.1.4 or newer