Yes it will, assuming the FLAC one makes sense to begin with. FLAC is a specialty codec tuned for compressing audio in the same way that DEFLATE is tuned for general (mostly text) files. Both of them are lossless, which means when you decompress the file you get exactly the same bits back as you started with.
So a correctly encoded FLAC file will be using CD quality audio or better. (CD audio is transparent when correctly encoded in 100% of cases.) FLAC is just a way to reduce the file size of that raw CD data by about 50%.
Lossy codecs like mp3 and AAC (the codec usually found in the m4a container) are also tuned to compress music, but they do so by throwing away a some of the original information. When this is done correctly it should still be transparent to the original the vast majority of the time. No one, not even an "audiophile", can tell the difference under any listening conditions. For mp3 (depending on encoder), the bitrate that achieves transparency is about 256 kbits/sec, though there are so-called "killer samples" that can break certain encoders at that bitrate. AAC (again, depending on encoder) is transparent closer to 192 kbits/sec. The state of the art has advanced remarkably since either were released: Opus is transparent in the vast majority of cases all the way down to 128 kbits / sec, and still sounds great at bitrates below that.
The problem is that just seeing the file extension gives you no guarantees about what the bitrate is. A 128 kbits/sec mp3 is going to sound like mush on a good system. If you convert that mp3 to FLAC it's still going to sound like mush, because you're using a lossy source. But a FLAC made from a CD will sound much better, as will a 320 kbits/sec mp3.
So if all you care about is transparency, getting 320 kbits/sec mp3s or 128 kbits/sec Opus files is probably good enough for you. The issue with "generational loss" I was referring to is when a lossy file is used as a source for another lossy encode. This is kind of like saving a file as a jpeg twice: you always lose more than just saving it once, even if the "quality" setting in the encoder is the same. Plus if you convert an AAC file to mp3, there's an even worse problem, which is that the different codecs try to compress the file in slightly different ways, which can lead to unexpected interactions and sometimes end up sounding like crap.
The point of keeping around a FLAC file is that you have a permanent archive of what was on the CD, and you have a source that you can use to make future lossy encodes from without the generational loss problem. All my albums are ripped to FLAC, but from those FLAC files I encode Opus files that are small enough to take with me on my phone.
