@manueljenkin
The transistors and other analog components in the amplifier and the dac (dac also has lots of gates) can be easily influenced by noise in the data, clock and especially ground lines and here we are looking at the output in a continuous spectrum and not merely threshold conditions. No simple way to correct these errors, actually no simple way to fully characterize and analyse these errors even. Arbitrary signal generation and fidelity is a very complex area.
You tend to complicate things, and with this approach it is almost impossible to understand the problem, because, as you correctly noted, we have a lot of areas in the computer where we can suspect problems. However, you forget that we can logically exclude the vast majority of these suspicions.
daс can be easily influenced by noise in the data, clock and especially ground lines
When we compare the sound of two identical files recorded on the same medium, when the player switches from one file to another, none of the above interference in the computer changes, that is, these interferences do not prevent us from making the correct conclusion about the sound of the compared files, all other thing being equal.
On the other hand, we can easily make sure that the intended noises do not affect the sound the way we hear it in our audio examples. To do this, it is enough during listening, for example, to insert and remove a USB flash drive from the computer, connect/disconnect the PSU in the laptop, start background hi-res video playback via Internet or any power consuming software, etc. If desired, you can come up with a lot of actions that will simulate serious changes in the level of noise and interference of the computer and conduct a simple but effective study of how your DAC reacts to heavy changes in the level and spectrum of interference emitted by it. Have you conducted such experiments?
To go into exact details of the modes in which the write environment affects the access noise profile, it'll require a deeper understanding into the actual physical characterization of the floating gate cells used (and most of this is proprietary and not visible to general consumers, includes me)
Here again, it is enough to simply analyze the situation, and not go into deep technical details. What do we have - the program loads a file into memory, presumably does something with it (in fact, nothing physically happens with the data) and writes the file back to disk. At the same time:
- This program does not work "at low level", that is, it cannot select a certain "low-noise" place on the disk and write the improved copy of the file to this place, since the physical location of files and folders on the disk is completely determined by OS.
- There is no code in the program that would analyze the disk surface for noise or anything else.
- Suppose different cells of the disk "sound" differently, then it is still unclear how the program, when repeatedly overwriting a file, makes similar changes in the sound (improvements or deterioration-it does not matter) for each copy. In theory, we should get an unpredictable result with each rewrite - either an improvement or a deterioration or non at all, and as a result, something indefinite in the end.
In my opinion, it is quite enough to stop clogging your head with noises and charges and start thinking of something else.