Hi - so when downloading via some sites I am given the choice between FLAC and WAV and I noticed the WAV file to be a lot bigger… so is there also a difference in SQ between the two (this would be really annoying - as I have done all my ripping in FLAC expecting this to be a lossless rip of my CDs)…
There is no difference, at all. Think of FLAC like winzip, but for audio. On playback Roon “unzips” the file back to the identical audio stream as the WAV and sends it to your Roon endpoint from where it is sent to your DAC.
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Cheers - the answer I was hoping for 
In ye olden days apple didn’t work with FLAC and some software wouldn’t pick up WAV tags so people leaned one way or the other. Nowadays all solved. 
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I would also add that in the olden days, computing power was lacking and FLAC with high compression could result in lesser quality playback on some devices. This resulted in tricking people to believe that .wav was superior to FLAC.
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Q… and I thought I have to re-rip all my CDs… 
The additional processing needed to decode back from FLAC to PCM (WAV) will increase some amount of noise and if it not done properly to reduce it before it goes the DAC, you will able to hear some minor different even though it is bit perfect.
In my experience, depending on the equipment used, I do hear some minor difference between FLAC vs WAV. I still prefer to rip my CDs to WAV and do some editing before I convert to FLAC.
So saving the files as WAV is better in terms of SQ according to your findings?
I knew I should have added “if anyone tells you otherwise you’d do well to ignore their ramblings” to my initial response.
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For archiving, it is preferable to save it in raw format. It can be use to do further editing and transcoding to other formats easily if needed. For playback, if You don’t have space constrain and want the best possible sound quality, WAV is still the best format for PCM. The same go to DSD, DSF is a uncompressed format.
Don’t waste your time using WAV especially if you are using an Endpoint instead of having your DAC connected directly to the Roon Core. Why? Because the endpoint is sent the same data regardless if the file was stored as a FLAC file or a WAV file.
Even if your DAC is directly connected to the Roon Core, the odds of you hearing a difference, if there is any, are minimal. Decoding a FLAC file is hardly a CPU intensive task. You are far more likely to have noise issues with the USB port than you are with the FLAC decompression process.
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Also, I would argue that you should archive in the most space efficient lossless format, FLAC, rather than WAV. Why? Because FLAC and WAV contain EXACTLY the same data, You can easily convert between the two formats and any other. You lose no data using FLAC.
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on top of that FLAC was designed to be lightweight to decode and it has built-in ability to check the integrity of the audio stream. But hey, to those that want to believe, WAV is where it’s at.
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If you want to spend an inordinate amount of time seeing how religious wars start; go to Google and type in WAV Vs FLAC. (it will automatically fill in “which is best” at the end)
If that doesn’t fill your days try
Cables, do they make a difference?
Digital Vs analogue…
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No, FLAC and WAV doesn’t not contain exactly the same information when it is not playback (not decode) or store in its static state, rather the end decoder will restore back the exact same data, something like a zip file.
Because FLAC is compressed in its static state, if there’s drop out during transmission or some loss of data due to corrupted file, the entire process cannot be reconstructed back in its original form, in some case it is not playable at all. FLAC typical compression ratio is about 1.75:1 meaning it is prone to 1.75x dropout even there only a few loss of byte.
Virtually all recording studios archive their masters in uncompressed raw format, because it is robust and durable, downside it will take up considerable space.
As far as I know FLAC contains metadata while WAV cannot. That’s not relevant for sound quality but a remarkable other difference.
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WAV can contain metadata. However there is no guarantee that the coded data can be read by another program.
“As a derivative of RIFF, WAV files can be tagged with metadata in the INFO chunk. In addition, WAV files can embed any kind of metadata, including but not limited to Extensible Metadata Platform (XMP) data or ID3 tags[28] in extra chunks. Applications may not handle this extra information or may expect to see it in a particular place. Although the RIFF specification requires that applications ignore chunks they do not recognize, some applications are confused by additional chunks.[ citation needed ]”
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The (audio) information within a FLAC encoded file would only be different from a WAV file coming from the same source if the encoding went wrong. Yes, the binary data at rest may be different but that’s what encoding is about. Or is your argument FLAC is in fact a lossy format? Then no further reading of my post is required.
Anyway if one has to decide if WAV or FLAC (or ALAC or …) will be the right format what may matter most is the actual use case and usage environment.
If you’re really archiving like a library and want to burden yourself with the task to preserve audio for generations (hopefully) to come then your choice may follow something like this https://www.loc.gov/preservation/resources/rfs/audio.html#independent - so no objection to the archival use case you mentioned. (*)
The average use case for digital home audio differs slightly though. It’s very reasonable to deploy current technical means - like lossless compression formats which also often support metadata more easily, something a librarian has other dedicated tools for btw. Storage space is limited, even if it seems to be cheap. And at least within the home network neither decoding FLAC (or ALAC) nor transmitting the encoded files should be a real issue so I don’t see an argument for WAV (or AIFF) here.
Sound degradation due to insufficient decoding isn’t really something one needs to fear. Roon for instance will as far as I do understand its workings decode the data on the Roon Core to LPCM and RAAT stream it to endpoints. So a loss can only occur when the FLAC or whatever file gets to the Roon Core device (local or networked attached storage) or if the Roon Core employed decoder is faulty. When pushed to the endpoints the audio is treated the same for WAV and FLAC sources because it is the same data.
As for playing with numbers: if on average 40% more storage space is needed how does it impact the likelihood of loosing some of that stored data?
(*) For a moment I thought I could mention here that something like MQA might be very bad from this point of view. A librarian who hasn’t full control about how or if the content to archive might get rendered later … but I leave that out. 
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So here`s the thing - I have ripped lossless FLAC files that I play via Roon and stream them to an Auralic Aries G1 Endpoint - should be fine, right?
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I’d say: yes.
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