Conclusion of Converting DTS-HD MA, TrueHD, LPCM to FLAC
Short version: Don't do this.
Gigabytes are cheap like a sand now. For each 1,000 gigabytes of compressing DTS-HD MA / TrueHD / LPCM to FLAC you will save 20 / 10 / 100 gigs accordingly.
For the most popular Blu-ray HD-audio formats like DTS-HD Master Audio and Dolby TrueHD the difference is almost none and equals only 2% or 1%. The main reason is that both of the codecs are already efficiently compressed.
But this is not the only reason, I wouldn’t recommend to recompress DTS-HD MA and TrueHD to FLAC. The second reason is that both codecs are proprietary. So you should ask yourself twice: “Am I absolutely sure to be married with FLAC permanently and make unreversible changes?”
And the last reason is the most scaring one. There is no “official” TrueHD or DTS-HD MA decoder or a specification. Open source decoders are really great effort, but they are reverse engineered. So adding a step to the process which possibly may cause a situation where your PC can alter the original audio because of proprietary codecs with closed standards is a nightmare.
So I highly recommend keeping DTS-HD MA and TrueHD audio streams intact. This assures the best quality and the best future-proof. Somedays If you decide to upgrade AVR and try bitstreaming, perhaps you will find how easy and great bitstreaming is and will be thankful that you ripped all Blu-rays with compressed HD-audio unchanged.
I doubt you have lots of movies containing uncompressed LPCM. But if you do and don't plan bitstreaming, you can go ahead and compress LPCM audio to FLAC for space saving fearlessly. This process is safe and reversible.
If somehow your AVR doesn’t have support of DTS-HD MA or Dolby TrueHD yet or you don’t have AVR, but still want to listen to HD-audio - you can go software way as alternative. Luckily there are solutions offering audio quality without compromise. There weren't issues detected with playing back TrueHD audio by variety of software players. And the most important is that open source DTS-HD Master Audio decoder appeared recently and actively developed now. It was already integrated to all well-known software such as multiplatform open source home theater Kodi (aka XBMC) and MPC-HC (via Lav Audio).
"Decoding" of the latest and the greatest object-oriented formats such as Dolby Atmos and DTS:X is still a problem for software. Software can't just "decode" Atmos or DTS:X, that's not how it works. Its not comparable to any audio codec you dealt with before. It effectively needs to be rendered based on the configuration of speakers in your room, which means it's unlikely to be easily supported by the existing software solutions for a long time to come.
Firstly, because developers have absolutely no idea how the Atmos and DTS:X data is structured, and secondly because they would need a lot of new code and configuration potential to actually be able to render the audio in a 3D space. If you want, consider it "3D Audio", which is fundamentally different than the previous "2D Audio" we used so far.
That's why even 'king of the hill' VLC player does not fully support Dolby Atmos playback at this point. And listeners have choppy audio issues with it. Regrettably, there is no workaround available. Yet. But sooner or later it will be found. Software / hardware are developing everyday. So that’s just a matter of time.