Ultimately, the SONOS player will render the file, regardless of where the file is stored or how the digital data is delivered. There is always room for mischief while transcoding. 

Hi @UNCMo96 

Welcome to the Sonos Community!

As stated in our Plex and Sonos help page, any FLAC file that Sonos does not support will be transcoded by Plex at up to 320Kbps into MP3. MP3 is lossy compression, not lossless, so there will be a loss in quality, though whether you’d be able to tell the difference or not is up for debate. It depends on your ears, frankly. If you can’t tell the difference, there’s no need to worry about it.

The FLAC files that Sonos does support will be played directly via Plex, without transcoding.

My recommendation (if you can tell the difference between FLAC and MP3) would be to do a one-time-conversion of all of your FLAC files that do not meet the Sonos supported format specifications listed on our Supported audio formats for Sonos music library page, into FLACs that are supported. It’s likely those with a sample rate above 48KHz or bitrate above 1536Kbps. Free software to do this is available, like Handbrake, for example. That way, all your FLACs will be played directly without transcoding and at the best possible quality on Sonos. Then, it wouldn’t matter if you used Plex or the Sonos Music Library - the quality would be the same, regardless - as @buzz mentioned.

If, after converting, you kept your original FLAC files in a different folder, you could point Plex towards that folder but not Sonos and then you’d still have access to those high-quality files for devices that will play them (though they’d show in Plex as duplicates - you might want to relabel them in metadata slightly).

I hope this helps.