When you decompress lossless data (FLAC) it shall be bit for bit the same as the original. There are enough checksum data in the compressed file to ensure this. Decompression software is able to recognize errors, and hopefully report them to the user instead of ignoring them.....
Regarding the discussion of sound differences between original CD, copied CD and hard-drive (given that you use the same DAC): Any differences in sound will come from differences in the digital material, which means that the copied CD is harder to read and the hard-drive is defect.
This is possible on an audio cd-drive because it has a logical preference to ignore reading errors so that the music can play continously.
However on a computer cd-drive reading errors will lead to retries until it is read error-free or the retry-count has reached it's preprogrammed maximum.